Is that with AI squadmates or real players?
This happens to real players, and it only seems to be just one squad member, last time it happened, it was always with the combat medic, although that I checked the editor to see if something was up, he was classed as Blufor NATO, same as the side selection on the server, but the moment someone spawned in the game as the medic, he became purple and was considered hostile for AI, couldn't get in to vehicles with us, etc.