A conceivable problem is that the game is set up so that a unit which is transporting other units does not defend first, even if it's the strongest (e.g. a caravel would defend rather than a loaded galleon).
i had a stack of transports w/land units and missile cruisers. ramesses attacked the stack and wiped out the transports. the mc's did nothing. WTH anyone know about this
my understanding from following the discussion in that thread is that in your case, if the mcs had missiles on them, and if the transports were empty, then yes that's by design.
Can you post a save or a screenshot showing the combat log?
yeah stealths don't admit that they're even THERE unless the "bad guy" has a stealth unit of his own in the area, at that moment, that can see them.
SDDs defending even when "invisible", and loaded transports defending in some/all cases, were being discussed at least as early as page 68. the thread is now up to page 75, and has several other topics mixed in since then. so your call whether to sort thru it or not.