There is no per se time that USNA publishes that is "disqualifying." That said, they do look at your mile run as one of the 3 key events of the CFA (crunches and pushups are the others). If you're a guy and run a sub 7:30, that's not great. Slower than that and it will be noticed. (For a female, add on a minute to those times). I'm NOT saying it's terrible or that candidates with those times have never been admitted. Just that you will be significantly slower than the average candidate.
USNA will probably look to what sports you do -- if you play varsity soccer, for example, they may chalk your results up to a bad day. If you aren't active in sports, the CFA takes on greater importance.
As noted, you can resubmit your scores. However, USNA won't/can't offer you an appointment until they have CFA scores reported for you. You have until March 1.
If you think your performance was: (1) bad and (2) a "glitch," then I would retake the test as soon as possible. If your scores are really bad and you're out of shape, that's a different story.
Finally, your BGO doesn't know what time is "disqualifying" as USNA doesn't tell us. Your RD can tell you whether scores you've submitted are passing. However, he/she won't tell you this until you've actually submitted scores and then only whether you have passed or failed (not if you've done well).