I have the same problem...

I hadn't considered this... I'm so sorry everyone. A new feature I'll be adding in the next few weeks would theoretically fix this problem, but I doubt I could have it done today. Let me see what I can do and I'll let you know when I've either fixed the problem or found a temporary solution until the next update. My apologies again...

Looks like I was wrong about implementing the feature today - I was able to complete it within only a few hours. :P I will make a full post about it later, but I've basically changed the way Level 100's function in battle (they can no longer receive stat boosts) and implemented a new "Reboot" function for all robots (allowing them to reset stats and re-level up from Level 1 again). This change may upset some, but I feel it's necessary to balance the game's final result.

I didn't encounter this bug when the new abilities came (Kinda helped I have no lv. 100 robots). When I tried to unlock Heat Man's Attack Burn/Blaze abilities by playing a mission, they just showed up after I beat my first enemy, no level up required. Fire Man's new weapons I got from a level up, but it was also from the first enemy I beat with him in a mission, so yeah.

Hey Spinstrike. I had this happen to me the other day so I'm aware of the issue - thank you. I think the unlock-abilities function is separate from the gain-experience function, so it's not checking to ensure you've actually leveled up that turn before looping through abilities and seeing which ones it should already have. I'll look into fixing this and update the thread when it's complete. :/