A few things I've found:
-EotH shipyards from level 2 onward do not spawn their light frigate garrison. It looks like they are still set to (try to) spawn Decimator cruisers, which AFAIK have been removed from the EotH roster and/or the game.
-EotH hangar spawns seem to be in reverse order. Which is to say, it's common for me to see Scarsiss/Furion spawns during Eras 1-3, but they then disappear from ship hangar spawns during Eras 4-5, when they should be introduced. EDIT: Some ships still spawn Scarsiss and the occasional Furion squadron in Era 4-5, including Stent's ASD. Unsure if it's a faction-wide issue or if it just affects specific ships.
-Thomork in the Crimson Empire campaign lacks a space map. The only way to fight there is via auto-resolve. EDIT: This is not the case with Thomorsk in the Deep Core campaign. Will try the CE campaign again to see if it's fixed.
-The IR AI can trigger early era changes just as the player can, but sometimes the option "persists" and can be added to a fleet, taking on the appearance of a damaged Carrack cruiser
-Not really a bug as such, but General Veers can spawn in the Empire during Era 3 at the same time that he may still be alive in the Eriadu Authority. As such, it is possible over the course of an era-progressive campaign for Veers to fight himself.
Pic related, thanks to a friend of mine for the meme.