The bot's can't handle cards that have you trash two cards from your hand.
If you play with something like Remake the bot will trash if they have one copper in their hand, but then will have to trash a second card that they need. I've seen a number of games where the bot ends up with under 5 cards in their hand because they keep trashing, and then it doesn't even know it needs to buy a copper to get out of it's hole.
The bots really should be balancing the % of treasure in their deck and it's value. it shouldn't be trashing for instance so many cards that it can't buy anything.
You guys hiring? I'm a programmer and would love to write my own bot.