That's not really a glitch, but you're right it's not the way that it "should" be. But actually, the program is doing exactly what it should. Confused?
What you are seeing is that those ships aren't getting forcefield protection, that's true. But, the reason for that is that they are in "cold storage" on a planet that you're not at (just the scouts, I see, which have no guns and so don't affect cold storage). Ships in cold storage are skipped from all calculations, which is why they aren't under the force field's protection -- this is critical for maintaining good performance with many tens of thousands of ships.
As soon as your ships with guns visit this planet, then all those AI ships come instantly out of cold storage, the calculations run, and then the ships are under the force fields as they should be by the time you'd actually want to shoot at them.
So... all is well.