So I only have 45 rep points but it says that I've earned the "Comment Everywhere" privilege. But under my account it says I need 50 rep points for commenting. Is there a glitch or something I'm not understanding?
You probably briefly earned this and then lost it—but the notification message was not removed from your inbox. Votes do get locked in so that people don't just randomly change their votes, but there is a grace period in the first few minutes after voting that allows you to un-vote or reverse your vote if you clicked on the wrong button.
I suspect somebody up-voted one of your posts (giving you +10 if it was an answer or +5 if it was a question) then thought better of it and un-voted before that grace period was up.
In any event I'm sure you'll be over the threshold soon enough.