A couple of turns after training a Frigate, I noticed that:
- The Frigate was parked in the middle of my city and couldn't be moved.
- All of the NPCs that had been stationed in the city were 1 square outside of it (exactly where they end up if you hit the Eject button on the in-city NPC icon).

I'm not sure what I did to get the Frigate from stationed to stuck. I was clicking through the units stationed in the city and may have right-clicked on/outside the city while doing that.
When I try to reproduce it from the previous 2 saves, the Frigate always ends up in the ocean (correct), including:
- Select the Frigate and right-click on city.
- Select the Frigate and right-click outside of city.
- Select the Frigate and hit the eject button.
- Shift-select everything stationed in city and right-click on/outside of city.
- Shift-select everything stationed in city and hit the eject button.
- Eject everything from city, one at a time.
Here are the saves. The city is "Point A" (first in tree):
Save #3 - Bug - Frigate stuck in city:
http://dl.dropbox.com/u/8067364/Beta_2a/Frigate-in-City/B2A-Frigate-in-city-cant-move.EleSav
Save #2 - Pre-Bug - Just prior to Save #3 (Frigate has just been trained and is stationed in city):
http://dl.dropbox.com/u/8067364/Beta_2a/Frigate-in-City/B2A-Frigate-in-city-cant-move-PRE.EleSav
Save #1 - Pre-Pre-Bug - Harbor in build queue
http://dl.dropbox.com/u/8067364/Beta_2a/Frigate-in-City/B2A-Frigate-in-city-cant-move-PRE-PRE.EleSav
EDIT: To clarify, Save #2 may not be the exact state prior to the bug (Save #3). I created Save #2 by loading Save #1 and replaying the steps I remembered (finish harbor, queue up Frigate and Transport, hit End Turn until Frigate finished). It's possible that the NPCs were (accidentally) removed from the city while the Frigate was in queue. It's also possible that the Frigate appeared in the city when it was finished (but I can't reproduce this either).
(The setup is a little odd because I made this game to test some caravan stuff)
I thought someone reported something similar in Beta 2, but I can't find the post.