After a user upvotes a comment, the option to flag as noise/offensive/spam disappears, while the up arrow icon "sticks" permanently. This has caused minor grumbling but is generally accepted as by design and not a big problem.
I just flagged a comment as noise for the first time. Afterwards, I moused over the comment and saw that the flag icon disappeared, which is slightly different behavior, but not a problem. However, the upvote arrow was still there. I clicked on it just to see if it was active, and my upvote was recorded.
The upvote option should really be disabled after a comment is flagged, both for the reason that flagging is disabled after upvoting and for consistency.