I appreciate the complete details you've shared, @pierau.

Let me share additional information to resolve this unexpected behavior when using the Project feature. 

It's possible that your clients were trying to add payroll expenses to projects by creating a bill. If you're using QuickBooks Online payroll, then the timesheets do not flow to projects because it will be tied to the paychecks. 

First, let's enter the employee's time. Here's how:

1. Go to the New icon (+).
2. Choose either Single time activity or a Weekly timesheet.
3. Select the name of the employee.
4. Set the Date Range or Pay Period of the timesheet.
5. Choose the Project or Job the employee worked on.
6. Pick the Pay Type.
7. Mark the Billable/hr tickbox.
8. Enter the hourly rate and the number of hrs the employee worked per day. 
9. Click the Save and Close button.

Once completed. you can now create the employee's paycheck. Just make sure to select the Keep these hours button when prompted to update the timesheet hours. 

You can read through these articles to learn more about how the Project feature works:

• Track income, costs, and profitability by project
• How to Use QuickBooks Projects to Track Project Income & Costs (w/ QuickBooks Online Payroll)

Keep me posted if you have other questions about using QuickBooks to manage your client's business finances. I'm always here to help.