I found a rather annoying bug. Nothing game-breaking, but still annoying.
So, I was able to reproduce this bug when splitting fighters. After splitting from the main ship their shields became useless, no longer stopping incoming fire from prisms (I haven't tested other weapons).
Here is also a save file: https://www.dropbox.com/s/ni64n067bvlqh6k/Ion%20bypass%20shield%20setup.savedgame?dl=0
When I would upload open the saved file after splitting the ships, the bug was no longer present, so this is a file of the fight before splitting.
So to reproduce the bug: Unpause the game, and wait for the shields to activate. Explode the charges of the orange ship named "Encircled" and observe the little fighters coming too close to "Goliath". you will quickly encounter the bug.