I think I might have found the answer to this. Inside of the rules for Ultimate Encounters, is the following: AFFILIATION & TACTICS
If a Team Tactic card refers to a character by affiliation, that character must be part of a squad using that affiliation. For example, if both players are playing squads with the Avengers affiliation, all Avengers characters may use the Avengers Assemble Team Tactic card when it is played.
So if I am reading this correctly, only the squad using MS as the affiliation could use that tactics card. The other squad was using Defenders, even though it had MS characters in it, and as such, it would not apply to them. Correct?