It makes sense to me. "Das stimmt" = "that agrees", interpretable as "that fits" or "that is true", nicht=not and ganz=entirely.
So "Das stimmt nicht ganz" is "That does not entirely agree" or "that is not entirely true" or "that is not exactly true".
That is not correct or exact does not carry the same meaning as that is not true, nicht wahr ?
I wich "that is not exactly right" would also be right. couldn't decide if I should use true or right... since I believe on the contectst what you would like to use, or how you choose to express yourself. In swedish we have a word "stämma" which I believe is equal to "stimmt" but we also have a word for right and true, so If you want to say "stämma" you have to choose which word to use...