When your total number of ships > ~700, the follow two problems occur:
(1) Most of your new ship pop-ups don't appear until on the right side of the screen, until you click the Menu button
(2) The ship list can only handle ~700 ships so when you exceed this point you won't be able to see all your ships.

Both (1) and (2) I've noticed in DL 1.2. Purge confirmed that (1) occurred in his last DA game but has not yet tried my work around of clicking on the Menu and then the Continue button. https://forums.galciv2.com/?forumid=346&aid=152317

(2) in my last DL 1.2 game I had ~4000 ships at the end and I read on the forums someone posted a game with ~17000 ships, so the ship list needs to handle much larger amounts than ~700.

The above has been e-mailed to gc2bugs@stardock.com and Cari Begle.