Welcome to the Community, @Alexuus.

Let me help and provide information about Retirement Contributions in QuickBooks Online Payroll (QBOP).

To begin with, QuickBooks Online (QBO) does not have a specific sequence for calculating payroll items. Any payroll item added to the program will be automatically calculated and included in the total. As a workaround, to prevent stipends from affecting retirement contributions, you have to create a separate paycheck for payroll items.

For now, I recommend sending feedback. Your feedback will help us improve your QBO experience and will be shared with our Product Development Team.

Here's how:

1. At the upper right corner, click the Gear icon.
2. Under the Profile, select Feedback.
3. Enter your comments or product suggestions.
4. Then, select Next to submit a feedback.

For more details about the feedback process, you can check this article: Submit Feedback.

You can also check this to track your request: Customer Feedback for QuickBooks Online.

For future reference, you can check this article to guide you in running payroll reports: Run payroll reports.

Please feel free to drop a comment below, if you have further concerns about the Retirement contribution or other QBO-related concerns. I will answer them in any possible way.

I appreciate the response, and I got an email from the Community wanting me to make this as Solved... however, this is not Solved.

QuickBooks Desktop Payroll has been doing this calculation correctly for us for 27 years... so QuickBooks Online Payroll went Backwards in development by at least 27 years!

That is not a solution.