Hi. I haven't bred Hermann's Tortoises myself, but have bred many Stars, Radiateds, and other tortoises over the years. One year old Radiateds are around 3"-3.5" and the same goes for Burmese and Sri Lankan Stars. Two year olds are 4"-5" and more in those species, but they are larger as adults, too.
Your tortoise may be just a bit small for its age, but the ones in the pet store seem very large for the ages they are describing to you. Do you think the ages they stated are correct? Also are theirs the same subspecies as yours? One type of Hermann's is much smaller than the other. Maybe that could be part of the difference.
Maybe some Hermann's Tortoise breeders could chime in with average sizes for one and two year old offspring they have raised and shed more light on this question.