The campaign anomalies that block ship types do so as a permanent wall to progression. For example, Cruisers cannot be used in the entire north-west area of the map, until Vandras IX is captured. The same problem is true for fighters in some areas. It’s a rather large impediment. Shouldn’t these anomalies be assigned to planets that will have less of a problematic effect? Or allow those ships to go there, but not take part in the battle? The fighters can’t even transit there as docked within Cruisers? It’s simply wrong.
No, it’s by design.
I can vouch that it’s vexing, until you realize it’s to force you to NOT just spam fighters for LITERALLY everything. just ~75% of it, like I do