Last game I noticed 2 bugs regarding Atlantis:
1. When I tried to build one I couldn't assist and the in built Atlantis couldn't be targeted etc.
2. More significant: somehow my Atlantis was invulnerable to subs. When I noticed that I surfaced it and submerged it again which fixed the bug. I noticed this before when an enemy Atlantis couldn't be killed by my subs. I was able to kill it with ground attack, though.
Edit:
Bug 1 @ about 25 min and
Bug 2 @ about 30 min