Ah I've never seen it happen before so I thought it might be a post-5.0 artifact but if it always happens it's probably fine.
Some observations of my 2 hours in a v5.001 campaign (80 planet simple style map, epic speed, normal ship caps, no expansions active & normal ship types)
Shield Bearers are still win machines when coupled with a few engineers. I started with them as my bonus ship & have unlocked mark II's. Using full cap of both mark I's & mark II's (24 & 22 respectively) with a full cap of mark II fighters, mark II bombers, full caps of all the free unlock starships & 3 mark I engineers I've yet to lose a ship when assaulting AI worlds. May want to look at reducing the FF radius they project as it's big enough that when one takes enough damage, another ends up covering it while the damaged one gets repaired.
My old lame tactic of using reclamators (Leech SS and/or Parasites if available) to build up a massive blob of free ships including types I couldn't build myself isn't possible any more due to the changes to the AI Eye & reclamators which is a good thing. AI Eyes in 4.0 used to be a walkover using that tactic as you'd reclaim units so fast you'd be able to just head straight to the AI Eye & kill it using the ships it spawned itself. I haven't got Parasites to play with yet but Leech SS seem to do enough damage to AI units that they are reclaimed with full health however I guess this is balanced in that they only fire one shot at a time.
MRS appears to be quite 'niche' now. May need it's knowledge unlock amount lowered from 4K as I see no reason why I would unlock it when I can unlock mark II & mark III engineers for the same amount of knowledge which are vastly more useful in v5.0 in my opinion.
Core Shield Generators are a great addition from what I can see. I haven't played long enough to get to an AI homeworld but I like how they force your hand with taking certain systems. I didn't particularly like the old mechanic of forcing you to kill all the guard posts in a AI core system before you could take out the AI core as it locked you in to a certain way to tackling the AI homeworlds.
My first ARS gave me Space Planes. Not sure if I like them or not yet. Also I've just unlocked mark I Riot SS as one of the AI's has Raptors which I keep having to send my Raid SS after since they like to kite. Hopefully the Riot SS will be able to pick them off or at least slow them down so I can kill them easier.
All in all, loving the changes. No complaints so far =)