one of the two bugs i have come across is ships disappearing. i had a titan and a kol battle cruiser, when i moved them they went to occupy the same space and the kol disappeared. its fighters were still in the gravity well and the drop menu said it was in there but i could not have it visible, attack or move. this may have something to do with the second bug.
the second bug is that ships and sometimes structures do not properly use gravity wells. they jump sometimes twice again the distance of the gravity well from the planet. furthermore, when I'm trying to build buildings (especially star bases) the gravity well and phase lines disappear and I'm stuck with a grid that encompasses everything.