Confirmed, My flagship/capital-ships vanished upon exiting phase jump. When selected, it shows a black screen. In a 3 hour game, this situation happend to me 4 times. (1 flagship, and 3 capital ships) 

I had something similar to this happen as well.  I played for a few hours last night and saved my game.  When I started it this afternoon, my Kol Battleship was missing.  I could find it on the plant's tab but could not make it go anywhere.  What's really neat is that I can't seem to destroy it either so it is taking up one of my capital ship crew slots.  I do seem to recall giving it an order to go somewhere right before I saved and shut the game down.

The game has looked pretty good other than this minor glitch.

Could it be an engine limit on polygon count or ship count or effects count, or something similar?

I warped in a fleet of 6 capital ships (3 Dunovs, an Akkan, a Kol and the new one, forget the name), my Loyalist Titan, and 6 Raloz Constructors into an extremely well-defended enemy grav well. The enemy had a Loyalist Titan, 5 to 7 capital ships, a large number of trade and refinery ships, tons of phase-cloaked mines, a starbase, about 15 squadrons of fighters, 30 to 40 combat frigates/cruisers, and a varied array of tactical and logistics structures, including a titan shipyard.

Immediately when my fleet arrived, both Titans started casting abilities like crazy, because my titan warped in extremely close to the enemy titan. I moved my Raloz Constructors away to keep them from getting eaten, and started building two starbases (Twin Fortresses research ability). I moved my capital ships in between an oncoming wave of enemy frigates+cruisers+corvettes+fighters and the places where I had ordered the Raloz Constructors to build starbases.

Very nearly at the exact moment when my second starbase began construction, BOTH Titans disappeared completely. I had zoomed out for just a second to check on an attack in another system, and as soon as I zoomed back in to the fight, they were gone! There was no indication that either ship was dealing or taking damage; no sign of ability use or weapons projectiles. All of my capships, starbases and enemy ships continued to fight as normal.

I then zoomed out of the gravity well to look at the ship consist summaries for the system, and as expected both Titans appeared in the list. Mine was at full hull and shields; the enemy Titan was at full hull and 39% shields. The numbers did not increase or decrease at all in the time that I watched them (about 45 seconds), suggesting that they were neither regenerating nor fighting.

I then tried to reproduce the problem with the already-busy system, suspecting some kind of resource overload, by flooding the system with dozens of Kodiaks and capital ships from other systems (I had Supply fully researched and a Supply Treaty with another empire by this time). I was unable to get anything else to disappear despite efforts to keep my ships and the enemy ships from destroying one another (to preserve the complexity).

So I really don't know what the problem is, because unfortunately I was unable to narrow it down. All I know is that my Titan and the enemy Titan are... somewhere not accessible. They still *exist* because I can't build another Titan, but their physical location is nowhere to be found.

I had a similar problem with pirates. Yesterday I capured some pirate ships with the new cap ship's boarding party in my own gravity well and it seemed to flag that gravity well as still having pirates in it even after I had moved my troops out. Later when I tred to select these phantom pirate ships from one of the menus I got a similar zoomed-to-empty-space issue as others are describing.

I am trying to recreate the circumstances but there was so much going on I am not sure what caused it.