The payments have to be in separate checks if i remember correctly. Always read the instructions. Google instruction for whatever the form number is and payment instruction should be at the end of the instructions.

I think you do not need to pay any fees for form I-821 for re-registration.

Fees for Registering for TPS for the First Time

Fees vary depending on the age of applicant registering for TPS. Please review the form instructions carefully before applying.

Read the Filing Fee and Special Instructions section on the Form I-821 page. These sections explain what fees to pay. If you do not want an EAD, do not check any of the three boxes at the top of Form I-765 where it states “I am applying for:”; leave all three boxes blank. Only check one of these boxes if you want an EAD. Refer to the chart under Special Instructions on the Form I-821 page for fee information.

Fees for Re-registering for TPS

There is no fee for Form I-821 if you are re-registering for TPS. You are required to submit the following fees when re-registering for TPS:

A biometric services fee if you are 14 years of age or older. See Form I-821page for details.
The Form I-765, Application for Employment Authorization fee if you wish to receive an EAD


https://www.uscis.gov/humanitarian/temporary-protected-status

OP has mentioned she filed for Initial Filing so $50 fee applies in her case

One big check is gud enough for a combo application. No need of separate checks. Could it be that the person reviewing the case wasn't updated with new fees or was he just being a douchebag? You might wanna call uscis and ask why they rejected.
Btw, did u write "US Department of Homeland Security" in payable to?

Hi, thank you everyone for responses.
Yes, I am a first time applicant hence $50 was included. Also, I did write "US Department of Homeland Security" in the 'payable to' section.
I tried to call USCIS but I cannot get through the computerized option of entering receipt number. Everytime I enter the receipt number (that's on the Rejection Notice), I get a message that says "Receipt number cannot be found at this time".