If you want generic squadrons you have to go into each squadron selection and select how many generics you want or else the points will be 0.
(Which is not a bug and works great but Is a new mechanic.)
I noticed yesterday, and did not check again today, that the Arkitten has a weird option for multiple defensive retrofits. Which is probably a bug, but doesn't really hurt anything since you should only select 1 defensive retrofit upgrade. It does look odd, esp if you do not understand that format (for multiple upgrades of the same type.)
I only built two fleets and then re-flushed them out with the new update, and the points worked perfectly.
The Arquitens is still only allowed 1 Defensive Retrofit by default, and it will flag the list as illegal if you select more than one. However, because it can be allowed two (by selecting Minister Tua), BS always displays the checkboxes. I wish it didn't, but that was the tradeoff for getting BattleScribe to validate the other copy of any given Upgrade card rule. Since the Arquitens is the only ship that can get a second Defensive Retrofit from Tua, that's the only place you see it in the Imperial catalogue (though a Pelta without the Phoenix Home title does the same thing with the Officer category in the Rebel catalogue).
All told, please keep up the feedback. I wouldn't have made the structural changes if I didn't think they were improvements, but it's possible not everyone shares my opinions. Also, a few of the changes were made for ease of use by data-editors, so you may have to take my word on those, but hopefully they will result in quicker future updates.