Hi! No, it's not the math, alternate choices or anything else. You can have a quiz comprised entirely of traditional questions and have it be off. I noticed (and commented on some time ago) the exact same problem. It's a system glitch (according to the fella I spoke to at Kaplan, who had no clue what to do about it). I routinely gave myself 25 question quizzes; close inspection of the "analysis" page would show me as having had only 24, or even 23 questions. Unrelated to the type of question I had, whether they were right, wrong, whatever.
Another treat you'll find is that it may tell you you got, say, 68% on a quiz, but when you do the math you'll find you got a 62%. I found my scores were actually consistently lower than what the computer tabulation popped out. On a couple of occasions it was higher.
So if scores are something you're stuck on, do the math yourself for the percentage. Otherwise, don't bother