I don't think there is anything wrong or unusual with your gar. It is just an observation. Gars with a dark base color actually seem to be more good looking in my opinion.
This is one of my Gator Gars (~6" and 8" now):
While I realize mine are just babies compared to yours, most Gator Gars I have seen on the Internet also seem to have a brownish color and are not very much darker than the ones in the picture above. (The spots probably go away with time).
I think the fact that the substrate in your tank is relatively dark is playing a part in this.