In the second E4 room, Kazuma's text has a typo: "extenguish" instead of "extinguish".
In the third E4 room, there's a Red Card Mimikyu. Red Card is supposed to work against the hit that breaks the disguise, making it a reliable answer to a setup sweeper, but the behavior here doesn't capture that effect. It only got held up on the first hit that deals damage after the disguise is broken, and if that hit manages to OHKO, then the Red Card never gets used at all, defeating the purpose.
Dragapult's Dragon Darts was able to hit 3 times; it's only supposed to be able to hit twice like Double Kick (but with a bunch of complications regarding doubles targeting).
If a Pokemon with Life Orb KOs itself with recoil while using a move like Volt Switch, it says (in the observed case) "Galvantula went back to Shane!" followed by the recoil message and the faint; it then faints without giving experience to anyone. As with the Healing Wish case noted earlier, this is not supposed to be able to deny XP for a KO. If a Life Orb user KOs itself with recoil from using a non-pivot move, experience from the KO does properly get awarded in that case.
Palossand's Water Compaction again gives a "drastically rose" message (3 or more stages) when it's only supposed to be a 2-stage increase, and thus "sharply rose" as the message.
The Darkoal quiz has a typo: "certin" instead of "certain".
The berry pocket in vanilla Emerald is designed to hold up to 43 different types of berries, because that's all that existed back then. With the later berries added here, it's possible to run out of room in the berry pocket, which typically isn't a big deal because the berry will remain there to be harvested later. However, browsing through the berry pocket, I see that it contains 46 entries, with the last two being "Toxic Plate x0" and "Lure Ball x0". These items can't be tossed, and despite the zero quantity, they can be given to a Pokemon as a held item, then taken off to be placed into the proper pocket, and the 0-quantity item will also remain at the bottom of berries, allowing for unlimited cloning of those items.
While it's not exactly a bug, the Battle Tower sells PP Ups for 1 BP and PP Maxes for 5. There is absolutely no point in getting a PP Max at that price, since you'd get the same effect at a lower price with 3 PP Ups--the opposite of a bulk discount.