Depending on who is calculating directory sizes, hard-linked files can easily get counted twice, even though they are really only a single inode and should be counted only once.
du terminal command is the surest way to find out how much space a directory is really taking. It never counts hard-linked files more than once.
(Caveat. If a file in directory A is hard-linked to a file in directory B, and neither directory is contained in the other,
du A and
du B will each count the file once, so you cannot just add the reported sizes together and get a meaningful sum. However,
du C, where C is a directory that contains both A and B, will count the file only once, arbitrarily deciding whether to count the storage as part of A or as part of B.)