This isn't a bug, although I can see how it might be unexpected. Comment upvotes do not add to reputation.
This is by design. Comments are intentionally second-class, because ongoing discussion is discouraged. The upvotes just help the good ones rise above the noise. You can, however, earn a couple of badges based on commenting — particularly, Pundit, for 10 comments with score of 5 or more.
You can also see an analysis of your reputation history at https://unix.stackexchange.com/reputation, and you can trigger a recalc if you think there's a problem.