Another thing that keeps happening is that queued up orders keep getting lost.
They recently tinkered with this bug for beta 2. Can you narrow down the exact steps on how to get them lost? The old bug was if a ship was on an auto-order (like auto-attack) holding down shift and queueing didn't work, the queue had to follow a manual order else it got lost.
If you notice it a lot, see if you can narrow down how exactly it happens, it'd be a great help.