They'd be locked out of the hospital wing unable to sneak back in.
Harry and Hermione had to get back to the hospital wing before Dumbledore locked the door, otherwise they'd be unable to get back in, and would be caught leaving the room when they weren't supposed to.
“Right, it’s nearly time,’ said Hermione tensely, looking at her watch. ‘We’ve got about forty-five minutes until Dumbledore locks the door to the hospital wing. We’ve got to rescue Sirius and get back into the ward before anybody realises we’re missing …”
It seems to be against the law for Hermione to use the Time-Turner for anything other than classes.
Hermione had a strict set of rules to follow when using the Time-Turner.
“But remember this, both of you. You must not be seen. Miss Granger, you know the law – you know what is at stake … you – must – not – be – seen.”
Professor McGonagall had to write letters to the Ministry, promising that Hermione would use it responsibly, only for getting to her classes.
“Professor McGonagall made me swear I wouldn’t tell anyone. She had to write all sorts of letters to the Ministry of Magic so I could have one. She had to tell them that I was a model student, and that I’d never, ever use it for anything except my studies …”
Using it to go against the Ministry to free Sirius Black and Buckbeak would certainly not be a Ministry-approved use.
Hermione may or may not have known what the exact consequences would be if she was caught misusing the Time-Turner, but she would have known it wouldn't have been good if the Ministry found out.