Well I've gone through them so many times I don't recall which ones I actually missed, but I believe any of them that didn't "count" were probably because I didn't save immediately after getting them and me assuming I actually had gotten them.
That said, I do know of a few that I totally missed or took me quite a while to find.
Tags (Numbers correspond to this map
#32 - Camouflaged in the wall just north of where a car pulls out of a drive.
#51 - Hidden in a dark, recessed part of the wall.
#96 - Camouflaged on an angled corner of the building.
Oysters (Numbers correspond to this map
#14 - Mistakenly assumed I had gotten, location is a bit off.
#21 - Location is a bit off.
#25,30,37 - Again, assumed done and incorrect.
#31 - Location is off.
#33 - Very deep!
#35 - Well hidden, assumed wrong again.
That's about it for what I can remember having trouble with. Are you sure all your tags "registered" with the "Doink!" sound? Did you mark any off that maybe you didn't save after??