So far (lol), I've seen that with the S11 patch, the following queues are now broken:
Starbase Fleet Defense, 20 man (Blue Space Bug, civilian vessels @ the start NEVER move, instance not completable)
Federation Starbase Blockade (Blue Space Bug, 100% Borg, still get rewards)
Federation Fleet Alert (Blue Space Bug, 100% Borg, no rewards) *this has been removed from the queues already, assuming it's being fixed.