With a time signature of, say, 4/4, it does not mean every bar must have 4 crotchets (1/4 notes). How could it? It would be a very boring piece rhythm-wise!
Each of those bars posted actually has the equivalent of 4 crotchets, and that's what counts - literally. The time signature tells how many of what, admittedly. But there are many combinations of notes which can be, and are, used to fill each bar - including rests. And once a time signature is stated, the writer is duty bound to keep to it, or change to a different time signature if the last one is inappropriate, which happens, although not that often in 'Classical' music, at least
So, this question is actually asked using false premises, but hopefully this answer will explain why.
EDIT: I guess you're considering the 4th movement, which has a time signature of 'C'. That in fact, is another way to designate 4/4, which may be where the confusion comes from?