Love the game so far, great work!
Ran into my first major Bug yesterday. Made it to Stage 3, was attacking a trolgar station and my "nemesis" jumped in. I blew him up and his pod warped out. When I jumped into the next zone the game became very laggy, I had zero lag problems before. I received a message that an enemy ship had jumped out, received the zone clear message but map screen gives no jump or wait icons meaning I will have to abandon the game, which is sad, as it's the most effective fleet I have managed to build. I tried everything up to a full restart of the iPad, but it looks like the save file keeps loading with the same bug.
Drawing on memory I may have jumped out of the initial encounter with the nemesis before his capsule warped out, then jumped back into finish the fight and he completed his jump out at that point. Hope this info helps.