I've bought two sets recently with either two left or two right arms on a single minimate. Then one of my Maria Hills has some surface warping on the torso. Also the occasional ill-fitting peg and that's it for the two packs. Nothing big.
Its the boxsets that appear more prone to problems. Tampo details faded, sometimes rubbing off, unusually flat finish, warped belts, gloves, & boots, cloudy paint, malformed torso inner structuring, etc. Problems I've never really had with the two packs. Primarily impacted for me were Thundercats 1, Femme Fatales 2, Spider-Man Friends and Foes, X-Men First Class, and Curse of the Mutants. Also comparing same minimates from the Universal Monsters boxsets and two packs, the two pack versions look just slightly better with better tampo transfers and glossier finish.
Fortunately I've had no missing accessories yet.