Not sure if this has been brought up, addressed, or if it's even the reason, but I am playing a game on an Insane map, with 4 AI. Around about turn 460, I started getting the 'Wait' hang issue. The Save/Load trick didn't work, but I think I found the issue.
Several of my Survey ships were near an AI Shipyard, and all of them were targeting it as their destination. I can only assume there's an anomaly/survey point under the shipyard. If I left-click on it to move them in it prompts me about going to war. As soon as I stood them down from survey, the Wait hang stopped, and the turn continued as normal.
I don't know if anyone else has had the issue, or if it's a known problem. If it's a new thing, might want to make it so the respawning anomalies don't show up under something else.