The IRS did not name the software companies that had the problem, but H&R Block said some if its customers were affected. Block said the company had resolved the problem.
Turbo Tax customers were not affected, company spokeswoman Julie Miller said.
The software omitted certain answers on Form 8863, the claim for the American Opportunity credit that provides up to $2,500 to help pay college expenses; and the Lifetime Learning credit that provides up to $2,000.
H&R Block said the forms were filled out correctly but the answers were dropped when the forms were transmitted to the IRS.
"It's important to note that the tax returns were prepared accurately. The error occurred in e-file processing," H&R Block said in a statement. "We are communicating directly with our impacted clients to assure them that we are doing everything we can to expedite their returns."
The IRS has long had a goal of increasing the number of people who file their tax returns electronically. The agency promises faster refunds for people who file electronically and have their refunds deposited directly into bank accounts. Most taxpayers who file this way can get refunds within 21 days, the agency says.
In 2012, nearly 120 million taxpayers electronically filed their federal tax returns with the IRS. That's about 81 percent of all individual returns.
The IRS expects to process about 150 million tax returns from individuals, so less than 1 percent will be affected. About 6.6 million taxpayers are expected to claim the education tax credits.
Taxpayers can check the status of their refund on the agency's "Where's my refund?" website.
The Associated Press contributed to this report.