"Isn't it enough that she's missing for three hours after the hospital said she was gone?" It was said about a girl who'd already been missing for three hours by that time. Why is it the Present Progressive not the Present Perfect Progressive?
If that's a line from a TV show, you will find that dialogue is written to reflect the fact that in real life, people don't always speak grammatically.
In a test situation, that should be "Isn't it enough that she's been missing for three hours since the hospital said she was gone?"