Here are a couple of issues I've run into recently. It's not an exhaustive list of bugs I've run into in this game, just things that happened recently so they're on my mind.
Sketch-related:
(1) Sketch targeting bug. This is probably the biggest issue of them, and also might be the easiest to fix. In official Pokemon games, Sketch can target anything other than the user, but in Uranium it targets only opponents (so, most notably, you can't use it on your ally in a double battle).
(2) Sketch PP-Up bug. Uranium lets you apply PP-Ups to Sketch even though they don't do anything (it keeps track of how many have been applied, and stops you after 3, it just doesn't change the number of PP). The official games have a sanity check that prevents you wasting PP-Ups in this way.
(3) Sketch Choice item bug. If you use Sketch while holding a choice item (whether it fails or not), you do not become choice-locked and can choose whatever moves you want for the rest of the battle. The way this should work (per official games) is that Sketch itself won't choice-lock you but you do become locked after choosing any move the next turn.
Other things:
(4) Duplicat/egg moves bug (if this is a bug). According to the Uranium wiki, Swabone can learn Glare as an egg move. To my knowledge the only parent that would work is Duplicat, which learns Glare naturally, but when I tried breeding this it didn't pass the move successfully. I'm not sure if Duplicat is meant to never pass egg moves, or not.
(5) Egg moves and Move Reminder bug. According to gen 6 mechanics, a pokemon born with an egg move should be able to relearn that move at the Move Reminder. This works in Uranium... as long as the pokemon hasn't evolved, but once it evolves that property is lost. (I tested this with Eevee and Synchronoise. If I overwrote it on Eevee, it still appears in the list at the Move Reminder. But when I evolved it to Flareon, it was no longer there. I also tested to see what would happen if it knew the move when evolving and forgot it later, to see if that made a difference, but no such luck, it's still not given as an option.)
(6) Nuzlocke mode earlygame crash. This was not discovered by me, but in a Let's Play I was following... basically, if you lose to Theo in the lab in Nuzlocke mode (very possible if you choose Orchynx, especially if you choose the "disable healing item use" clause), there's no game over (I think the scripted events where the professor talks about the battle etc take precedence) and you end up leaving with only the "dead" starter in your party. When you encounter a wild battle or trainer after that, the game will crash when it tries to send out a pokemon. I'm kind of shocked this managed to remain unnoticed for so long, there really should've been a sanity check added.
Edited to add: Just thought of another one.
(7) Nuzlocke mode pokeball bug. I've noticed that in nuzlocke mode, when you try to use a pokeball and get the "But $PLAYERNAME already caught a pokemon on this area!" (sic) message, the pokeball will still be used up. I found this rather frustrating, especially as I would often go there to check when I wasn't sure whether or not I was allowed to catch something (it's not always consistent what counts as an "area" for the purposes of nuzlocke, I've found). Truthfully I think the main thing this tells me is that Nuzlocke mode needs some kind of visual indicator of when a pokemon is legal to catch, kind of like the pokeball icon that's used to show whether you have something registered in the pokedex.
Second edit: here are some more.
(8) Sound volume issue. The jingle that plays when you successfully catch a pokemon always plays at max volume regardless of where you have the volume sliders set. (This is the only one I've personally observed, I suppose it's possible other things could be affected too.) I don't think it's a generic "sound effects" versus "music" issue, because other sound effects (e.g. from moves) do act as expected with the volume settings.
(9) Copycat. This move doesn't appear to do anything, regardless of circumstances. I've mainly noticed this because I've been fighting a lot of duplicat recently; I have not tried using the move myself to see if it behaves differently when used by the player.
(10) Issues with trading and pokemon's "obtained location" and obtained level. This actually might not be something that is possible to fix, depending on how the save structure is set up. In the official games, when you trade a pokemon, it doesn't actually change any of this information, just masks it if you aren't the OT (some games even still displayed it, just with slightly different text, e.g., changed "met in X location" to "probably met in X location"). In Uranium it's actually overwriting, so even when trading a pokemon away and then back to the OT, it will change to "Faraway Place" and "Traded at Level X" (let's also note that that level is probably incorrect, because that doesn't seem to get edited, so if the pokemon was hatched from an egg it will always display as "Traded at Level 1" even if it was, in fact, leveled up before trading).
(11) Window recentring bug. I know this was fixed in most instances (e.g. the options menu), but it still happens when changing files on the main menu screen. If you've moved the window and then go to swap to e.g. the second file slot, the window is still moved back to the centre of the screen.
Sketch-related:
(1) Sketch targeting bug. This is probably the biggest issue of them, and also might be the easiest to fix. In official Pokemon games, Sketch can target anything other than the user, but in Uranium it targets only opponents (so, most notably, you can't use it on your ally in a double battle).
(2) Sketch PP-Up bug. Uranium lets you apply PP-Ups to Sketch even though they don't do anything (it keeps track of how many have been applied, and stops you after 3, it just doesn't change the number of PP). The official games have a sanity check that prevents you wasting PP-Ups in this way.
(3) Sketch Choice item bug. If you use Sketch while holding a choice item (whether it fails or not), you do not become choice-locked and can choose whatever moves you want for the rest of the battle. The way this should work (per official games) is that Sketch itself won't choice-lock you but you do become locked after choosing any move the next turn.
Other things:
(4) Duplicat/egg moves bug (if this is a bug). According to the Uranium wiki, Swabone can learn Glare as an egg move. To my knowledge the only parent that would work is Duplicat, which learns Glare naturally, but when I tried breeding this it didn't pass the move successfully. I'm not sure if Duplicat is meant to never pass egg moves, or not.
(5) Egg moves and Move Reminder bug. According to gen 6 mechanics, a pokemon born with an egg move should be able to relearn that move at the Move Reminder. This works in Uranium... as long as the pokemon hasn't evolved, but once it evolves that property is lost. (I tested this with Eevee and Synchronoise. If I overwrote it on Eevee, it still appears in the list at the Move Reminder. But when I evolved it to Flareon, it was no longer there. I also tested to see what would happen if it knew the move when evolving and forgot it later, to see if that made a difference, but no such luck, it's still not given as an option.)
(6) Nuzlocke mode earlygame crash. This was not discovered by me, but in a Let's Play I was following... basically, if you lose to Theo in the lab in Nuzlocke mode (very possible if you choose Orchynx, especially if you choose the "disable healing item use" clause), there's no game over (I think the scripted events where the professor talks about the battle etc take precedence) and you end up leaving with only the "dead" starter in your party. When you encounter a wild battle or trainer after that, the game will crash when it tries to send out a pokemon. I'm kind of shocked this managed to remain unnoticed for so long, there really should've been a sanity check added.
Edited to add: Just thought of another one.
(7) Nuzlocke mode pokeball bug. I've noticed that in nuzlocke mode, when you try to use a pokeball and get the "But $PLAYERNAME already caught a pokemon on this area!" (sic) message, the pokeball will still be used up. I found this rather frustrating, especially as I would often go there to check when I wasn't sure whether or not I was allowed to catch something (it's not always consistent what counts as an "area" for the purposes of nuzlocke, I've found). Truthfully I think the main thing this tells me is that Nuzlocke mode needs some kind of visual indicator of when a pokemon is legal to catch, kind of like the pokeball icon that's used to show whether you have something registered in the pokedex.
Second edit: here are some more.
(8) Sound volume issue. The jingle that plays when you successfully catch a pokemon always plays at max volume regardless of where you have the volume sliders set. (This is the only one I've personally observed, I suppose it's possible other things could be affected too.) I don't think it's a generic "sound effects" versus "music" issue, because other sound effects (e.g. from moves) do act as expected with the volume settings.
(9) Copycat. This move doesn't appear to do anything, regardless of circumstances. I've mainly noticed this because I've been fighting a lot of duplicat recently; I have not tried using the move myself to see if it behaves differently when used by the player.
(10) Issues with trading and pokemon's "obtained location" and obtained level. This actually might not be something that is possible to fix, depending on how the save structure is set up. In the official games, when you trade a pokemon, it doesn't actually change any of this information, just masks it if you aren't the OT (some games even still displayed it, just with slightly different text, e.g., changed "met in X location" to "probably met in X location"). In Uranium it's actually overwriting, so even when trading a pokemon away and then back to the OT, it will change to "Faraway Place" and "Traded at Level X" (let's also note that that level is probably incorrect, because that doesn't seem to get edited, so if the pokemon was hatched from an egg it will always display as "Traded at Level 1" even if it was, in fact, leveled up before trading).
(11) Window recentring bug. I know this was fixed in most instances (e.g. the options menu), but it still happens when changing files on the main menu screen. If you've moved the window and then go to swap to e.g. the second file slot, the window is still moved back to the centre of the screen.
