I'll go with an example.

My cap ship is under attack and I got to run away, so I order my ship to phase jump somewhere else.
Phases jump is initialized and then the opponent uses an ability to disable all ships functions and make it invulnerable. Once the ability times out, I expect my ship to re-initialize the jump. But, since my ship was interrupter while charging the phase jump, it won't resume automatically. I have to reorder it to do it. Instead, it jumps backs into battle.

It's quite annoying because if I order a ship to jump away, I don't expect to have to keep an eye on it in case it suddenly return into the fight which I wanted to leave.

Maybe the game intend to work that way to punish cowards?

Found while playing 1.03