[Rothgar]

I heard of that bug a long time ago, I have not heard of any problems since? I actually ran into it with CS:GO not Source, you might want to make sure you are running latest SourceMod/Metamod/AFK Manager plugin.

The plugin basically just uses the SourceMod ChangeTeam functions, I can't really comment on whether this type of issue might be caused by Valve doing some additional property changes in addition to moving of players or whether SourceMod might need to review the Change Team functions to see if it needs to be updated but in theory the method used to move players should be the same as if a player changed team themselves in their game client, it's just being handled Server side.