Until 1990, mintmarks were added to the dies by hand with a punch. So there will be some slight variation to where the mintmark is located, as well as being possibly being slightly tilted. As long as the mintmark is in the right general location, there is no additional value. Sometimes they may actually touch the numbers in the date, and that can bring some additional value. As far as differences in size, it could be due to die wear,
Struck Through Grease, or damage. A picture comparing the two would help determine what is going on.