The title basically says it all. I submitted a run but realized that the timer in the video was messed up. The end time is correct but when timing, the hour overlaps with the minute. Is this fine for the submission?

It doesn't matter what the timer shows in the video* as long as you submitted it with the correct time.

*Obviously this depends on the game's community since each game sets their own rules, but in most cases it won't matter.