Chronic minor issues I've seen:
Pits on front of Fed engines, easily fixed with some putty.
Roughness on the casting for the Fed nacelles, requiring significant smoothing out, along with some mold misalignment. This is less common than it used to be with the resin models which were horrible in this regard.
Some roughness in the texture of the Fed saucers. Some have needed some minor putty around the bridge area to smooth out a bit.
EVERY E4 model I've gotten had major problems with the right engine and wing; I suspect the mold is to blame here. ALL have needed significant TLC to get looking barely acceptable.
MOST Fed CA/CC/BCH/DNG have needed major work on the engine pylon ends and hull socket to get them to fit together well enough to be glued. The Fed POL are horrible in this regard.
Fed DNG attachments for the center engine have been difficult as well.
Some Klingon cruisers have been problematic getting the engine/wing on; the D6/D7/C7 series usually need some work. Sometimes I can superglue-gel the engines on, sometimes I have to resort to epoxy. Generally the D5 engines go right on with superglue gel (tighter fit). I have noticed the D5's engine/wing seem to have nicer molding/even has grooves for the glue to stick to.
The Klingon C8 has needed the most work, with the holes in it, removing the injection sprues, and fixing minor bubbling. BUT it also is better than the early resin one, which took alot of work to fix up.