Did you say in the report that the register receipt was wrong? In addition to showing the times I entered and left, it there is anything wrong with the receipt, I always say something like "Although the date was shown correctly, the receipt incorrectly showed 11:59, although it was 12:04 when I paid for my order." Many times with a number of MSCs, the receipt has been wrong and I have so far always been paid. One time a receipt showed Thursday at 2PM when it was really Friday at 6:47! I told them in the report and I was paid and no questions were asked. But tell them. Don't wait for them to find it and come back and say you did it wrong. Tell them you did it right and the time is shown incorrectly. That shows them that you know there is a discrepancy.
I can't even count the number of times a receipt has listed a time that is not correct, and quite often they are wildly off. I have one location I hit every few weeks that is always almost 2 hours off. I've been lucky that none of my shops have been invalidated because of that, but I'm hoping that if they ever had a question they'd ask me first to explain the difference.
I live in an area that does not participate Daylight Saving Time. Often times POS software does not know this and automatically changes the time twice a year. I try to outline this as a possible cause for the discrepancy if that is the case.