Maybe been said, but nearly every "time clock" monitoring program goes by 15-minute (really 7-8 minute) increments—from 8:00 to 8:07, you clocked in at 8. From 8:08 to 8:22, you clocked in at 8:15 etc …
So, you get some extra, or you get some taken away.
If yours is "to the minute," then I would take a 3-minute shorter lunch and be done with it.
But I would also review my time, and if I had ANY minutes over, I would expect that overtime pay.