Ok, found another miniaturization related bug.
When Advanced Miniaturization is completed, every engine gains +1 to its size as well, thus negating the effect for some ships I use.
After another Miniaturization tech is completed, weapons are given a +1 to size as well (engines may gain another +1 sometime, but not sure), at least I think I've seen this. I can't remember after which tech advance this happened at.
I definately remember the engine size going up 1 since an Impulse Drive Mk3 was a size 7 for a transport hull, after Advanced Miniaturization, it went to a size 8, thus making some of my transport hull based designs overmaxed. Go figure...