Oh yuck I can well imagine how aggravating bugged research must have been. I also get why they made torpedoes unusable above water, since not all underwater munitions function out of water. However, if we know it's a terror mission above the surface of the water, why don't we have more conventional RPG weaponry? I get that the Coelacanth's weaponry is too different to be modified on the fly, but there's no reason why an Aquanaut can't simply grab an old rocket launcher.
I also had a gripe that naval base terror missions featured unarmed sailors. FFS it's a naval base don't they have guns too? I know they didn't want to make it easy on us but I would have loved to see something like the sailors fight back even if they were just using pistols. Look at how Apocalypse gave us Megapol, or the Enemy Within DLC added Security Personnel, or Xenonauts added in friendly NPC allies like local police and military forces. I wonder if it was just a limitation to the engine at the time?
I hope it doesn't seem like I'm just bitching here I love the X-com series but those gripes have always stuck with me.