With very large fleets it can sometimes happen. The number is 90%, I think. But since capital ships are pretty big, with a very big and packed fleet it's possible that they bump into other ships and have a hard time aligning for jump - which can sometimes result in them being shunted to the 10% left behind.

Hmm, do you have a replay or a save game of it?

Why does everybody with a bug complaint say this?

Mainly cause for me its gamebreaking. I literally cant play the game. Before the 1.4 patch everything worked fine now it doesn't. Anyway heres the file if it doesnt work just give us a yell.

http://www.wikiupload.com/download_page.php?id=62312 

To the right in the yellow box there is a download file button that should be it.

Fleet phase jumping is wonky, the paradigm needs changing.  Make a bubble, ships in the bubble phase, if they miss it, they take the next bubble.

Higher tech means the bubble is bigger, faster.

As it stands now, phase jump behavior is comical and worse: unreliable.