Well, I'm a fucking retard... -_-
I decided to get off at Rutherford since I needed to pick up some things, and figured it would be easier to find something at 16th and Yonge instead of Major Mackenzie and Yonge. Also according to Google a bus would only be about a 5 minute wait.
So at Rutherford, in a momentary laps of reason, I decided to press the override button and tap. The only thing I can assume is that I thought that if perhaps it did pick up a tap at Union, it might clear it. As for pressing the override button, I have no god damn clue. Perhaps I thought it would do nothing since I don't have a default set?
Anyways I didn't want to miss my bus, which on weekends I have to walk across a parking lot to get to, so I didn't go back to try and correct. Of course the bus was 10 minutes late, but whatever.
When I tapped on the YRT bus it said I had $14 left on my card. I did the math and I should have about $19 left, so I guess it took the $5 when I tapped with override. I also assume that it will take an additional $5 since I cannot tap off in Barrie.
I called Presto up, and the rep said I had to call GO. Hopefully they will understand the situation and credit me back, especially since I tapped on a YRT bus 15 minutes after tapping at Rutherford, but I can kiss my free trip on the Barrie line goodbye now.