Thanks to Moo again for giving me another valuable heads up. Moo said that his progress showed that he'd worked out for around 7 hours but that he knew he'd worked out for close to 11 hours.
To fix this bug I first checked all the timers in the game which appeared to be fine. So I went over the save system and found the bug there. So I restructured the save system and the bug is no more.
The bug kind of made players workout more than they needed to in order to unlock rooms and ranks, so it is maybe the only computer bug in the world that has helped people to get fitter lol.