I have run into a specific queuing issue a few times from playing the current Beta the last few weeks. My ships will not queue a phase jump if their current action is attacking an enemy ship automatically.
This might be best explained in an example:
My ships in a sector are cleaning out the militia. I zoom in on the sector and they are currently attacking ship X. I queue them to then attack ship Y and Z, and then try to queue for them to jump to an adjacent planet once they have done this. The 2 queued attack commands are given successfully, but not the phase jump.
The work around in this situation is to select my ships and order them to attack the target they are currently attacking and then proceed to queue up the same commands again. In this situation, the phase jump is successfully added to the queue.
So essentially, if their current command wasn't specifically given by me, the queued phase jump won't work.