I have encountered this bug as well. Was using Everyone's Best Friend, Unlimited companion ammo and More Smarter Companions. The last one on that short list conflicted horribly with the Best Friend Mod. Made Danse attack me at the Cambridge police station. Ended up with the "Check your fire" bug after but was able to advance with console commands, however in Arcjet he entered and immediately let the building. No companion has followed me through a loading cell since. Previous saves are now bugged as well though they used to work, even after removing all companion based mods. The problem started for me about a month ago. I have gone through everything but can't figure this one out. It is definitely mod related. Removing all mods and starting a fresh game works, but yeah, what's the point. Sadly this is downright game breaking to me. I may be done as I just don't feel like spending more time on this. Will check back once in a while to see if there is any progress though. Maybe someone will figure this out.