During transfering the player to the other team AMX X is sending the message TeamInfo - so all other AMX X plugins can handle, the player is now in the new team. Unfortunatelly, if that message is just sent by any of metamod plugins, the metamod is blocking that message to be send to other mm plugins, so none of them (like metamod bots, like StatsMe, like AdminMod etc) can know that (since they cannot see blocked messages).
The only way to do this right is - switch the player to the other team and just respawn him (for example in the Spawn area of the new team). Then the right TeamInfo message is sent by the game Engine, which is catchable for all metamod plugins (also for this bot).
More info read here:
http://forums.alliedmods.net/showthread.php?t=51171
[EDIT]
And this is not a bug in podbot mm, but You didn't need to know that. I'm moving the question to Common Questions forum.
[/EDIT]