The new moves that you insert in this hack still have the old description of the moves you replaced. My bagon learned Dragon Pulse and in the description it says it always take 40 hp damage something like that. Thinking it is a weak move I cancelled teaching it to my bagon. Then, here comes a rival battle and his dragonair is 1-hit KOing my pokemons using Dragon Pulse which I expect to only inflict 40 hp damage. There are also other moves like this like zen headbutt.
Another bug I encountered is the events are repeated when you return to that place. Example is the Brock with Entei and the battle with professor in the battle cave.
Overall I'm enjoying this hack because the difficulty is very challenging.