Currently playing on a spiral galaxy with about 336 ships and/or fleets on my list. All my colony ships and constructors don't show up on the ship list. I know they're on the map because my waypoints show them on the way and I can eventually find them on the map and move them. This was before the new update which just downloaded a few minutes ago, but they still don't show. I think a survey ship or two is also missing from the list because they are definitely ships that I control manually and every turn, I find myself in an unexpected battle with pirates when claim an anomaly. 

Somebody needs to do some work on the ship list because it hasn't really been reliable since day one. It does NOT keep a sorted order whenever you build a starbase, make a fleet, etc., etc. With a complex map and a need to use a sorted list by name, it takes about 1200 clicks to move 300 ships. Sort, select ship, move, claim anomaly, recover pirate ship from battle, oops-list is gone. Resort, resort again to get same order, scroll through list to find same ship, move to next ship, etc., etc. Did nobody at Stardock hear of list pointers?

I realize nobody will actually fix this because it's not a fix that will ensure a monetary gain but it would make the game at least 50 times faster. And actually more playable. (Speaking as somebody who has 5500+ hrs. in the game).