On 3x way servers, things can seem confusing concerning allies and whatnot. Let me explain. If you are ISC and take a mission in a klink hex, then your allies may be either yours or that of the Klingon enemy, which could be any of the Alliance races. You can then say the two sides have a mutual interest in seeing the enemy destroyed. Scripts are hardcoded this way. They have side A and B. Whosoever is on side B must be the enemy of team A. Figure that out.
Now if you say that u attacked the Klink hex and had a Fed enemy combatant in addition to a Klink combatant, that shouldnt be possible. Please report the mission and sides including ships seen. I'd like some more info on what happened. I'll get on and test as well.