Astronaut sim leaving work early and not getting paid

There are two things you can try.

1. Reset your Sim with the resetsim cheat code in the cheat console. To open the console press [Ctrl] + [Shift] + C - after that type resetsim <first name> <last name> into the console. For example: resetsim Jane Doe

2. If that does not help, make them quit the job and get it again. I know that's a little annoying as they have to start with the level 1 job again, but as they already have all the required skills they should get promoted rather fast.