Well, I was doing a run in the kestrel, on the iPad edition, and had got to the flagship fight. I had just jumped to the flagship, and stage 1 was starting, when I saw the flagship had only THREE shields, not four. I fought the flagship, and my burst laser 2 took down it's shields, allowing me to hit it with a pike beam, so it wasn't just visual. I defeated stage 1, and the same thing happened with the other two stages. Also, not sure if relevant, but none of the ships I saw in that run had four shields either. Does anyone know anything about this?
Note: I did manage to get a screen shot of the flagship with three shields and a undamaged shield system, but I'm not sure how to post it, so any help with that would be good.