Brian Johnson had no issues getting the $800 advanced child tax credit (CTC) payments in July and August, the first two months the payments were disbursed.

But then in September, the 44-year-old's family was one of many that did not receive a direct deposit on the 15th, when the IRS originally scheduled them to be paid out. A few weeks later, he received a $500 direct deposit, $300 less than the total his three children qualify for each month.

Soon after that, he received another $500 check in the mail from the Treasury Department, meaning he had now been overpaid. With some exceptions, taxpayers will owe back any excess payments when they file their 2021 tax returns.

The Wisconsin resident expected that his family would simply receive $200 less this month to make up for the overpayment. But when his wife checked the IRS CTC portal this week, it says that his family is set to receive just $367 on Oct. 15th. The math, he says, isn't adding up.

"If you don't opt out of your advanced child tax credit payment, nothing else should affect it," Johnson tells CNBC Make It. "To see this odd dollar amount is really bizarre."

He is one of many parents confused by the IRS's rollout of the advanced CTC payments this year. While he is grateful for the extra cash and acknowledges it is a big undertaking to send it out each month, he says it's difficult to plan to use the money when the amount of the check and the date it is delivered has varied so much month-to-month.

"We're supposed to be able to count on it," he says. "Now I'm worrying, am I going to have the money for this cellphone bill, this car payment?"

Last month, the IRS said a technical issue resulted in around 2% of CTC recipients not getting their September payment, primarily those who had recently updated their bank account or home address on the agency's CTC portal. The agency also said that monthly payment amounts can change "depending on recently processed tax returns." The agency did not immediately respond to a request for comment on this story.

Other parents tell CNBC Make It they still have not received September's payment, and worry that means they also won't receive October's on time. Families have struggled to reach the IRS to ask for help.

Megan Lewis, 42, has still not received the $300 September payment for her 3-year-old daughter. The North Carolina resident says she and her husband have had to dip into savings to fund preschool costs that they had expected the CTC payments to cover.

"I know it's only $300 a month, but for the people who need it most, it's a game changer," Lewis says. "I thought the point of the CTC was to get money into the hands of parents now." 

Johnson says after more than a year of sending direct payments to families, the agency should have the kinks worked out of the system.

"Don't tell people to be able to count on it if they can't," he says.

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