Autopilot gets them into space and it fails in transit?
I don't think you understand how hard it is to accidentally hit a planet. As always (when dealing with an issue that can be addressed with this specific quote), Douglas Adams said it best:
Space is big. You just won't believe how vastly, hugely, mind- bogglingly big it is. I mean, you may think it's a long way down the road to the chemist's, but that's just peanuts to space.
Side note: Would such a quote be considered the best response if it hadn't been put in a famous sci-fi book? Is there any way to know for sure?
Military ship could just have orders to disable any nonmilitary ship detected to prevent convicts from getting offplanet,
Hardly intelligent orders. Especially since spacecraft would
A. not be in the manufacturing capability of these people for decades
B. be easily-detectable at extreme distances, allowing easy identification of origin.
if it is a small starhopper transport then it could run with a single person and the autopilot.
...but would have minimal ability to store supplies or house hydroponics. Among other issues.
The guy could be planning on rescuing someone,
Have you heard of "Opsec"? The military has, and it would be in full force here.
the ship could have had a transit failure and come out too close to the grav well and been disabled...
All the more reason for the military not to indiscriminately shoot at any ships near the planet!
P.S. See "Space Is Big" for reasons why this is incredibly unlikely for any transit that is capable of going anywhere of note without hitting a gravity well first.
the military could be required to maintain a presence in the system
By whom?
or it just could be bad timing
"You'd better watch out for hungry
T. rexes. With bad timing, one could eat you!"
Actually, this makes MORE sense than your argument, because there actually is a bad time that would make these chances measurably large (the late Cretaceous).
and if the ship was close enough to the planet when it finished transit then it could crash before the atmosphere completely leaked.
...?