Employee cannot log into his quickbooks time: the message says "you were signed out due to no associated companies with your user" ?

I appreciate you letting us know about this, Nick. I'll point you in the right direction to sort the error prompt received when accessing QuickBooks Time (QB Time) through the mobile application.

To resolve this issue, I recommend seeking assistance from our Customer Care Team. They can access the account in a secure environment and perform a detailed investigation to identify the cause of the error message. Visit this page and select QuickBooks Time to get help from our Team: quickbooks.intuit.com/learn-support/help/en-us/contact-us

For visual reference, see the screenshot below: 

Moreover, you can check this page to help manage employees inside the program: Add and manage team members for QuickBooks Time.

I'm here to help with handling employees or their information inside QuickBooks. If you have more questions about the program, please use the comment section below so I can respond as soon as possible. Stay safe.