Well, not having any details we could only speculate. It's possible that bots could be written in a way that assumes they're the only bot loaded, causing them to interfere with another bot in several ways:
1. by blocking the other bot from seeing events it needs to see.
2. by seeing events intended intended for the other bot.
3. if both scripts use an alias given the exact same name, there are cases where one bot would be executing the other bot's alias.
4. if both bots use the same !keyword command, depending how the script is written, either 1 or both bots could see it. They often try to avoid this kind of problem by responding to commands that begin with their nick, but if you're loading them in the same server connection...
It might be possible to solve your problem by running 2 instances of mirc not sharing the same mirc.ini and probably not the same same folders. It's likely not good enough to open a 2nd server connection in the same mirc using a different nick because they would both be seeing the same list of scripts having the same events being intercepted.