The first tax season with Obamacare is drawing to a close on April 15, and "surprises" in some taxpayers' refunds may affect how many people enroll in health insurance through the program in the future, experts said.

President Obama's healthcare law offers subsidies in the form of tax credits to help individuals purchase insurance. The credits are available either when they sign up for coverage or as part of their tax refunds. Because the credits are calculated based on income, for those receiving financial assistance in advance, any changes to earnings between the time individuals apply for Obamacare and the time they file taxes could mean they have to pay back some of the subsidies by forgoing all or part of their refunds.

Tax preparer H&R Block has estimated about 52 percent of Obamacare customers who received advanced credits will have to pay at least part of them back.

Experts said that the process of matching Obamacare tax credits with reported income, known as "reconciliation," could have an impact on enrollment.

"Some unexpected surprises could make more people skittish," said Larry Levitt, senior vice president of the nonpartisan Kaiser Family Foundation. "I think the better response would be for people to be conscientious about reporting changes in income throughout the year, which would minimize refunds or repayments."

But that can be hard to do.

"People did their best to comply and found out they got screwed anyways," Doug Holtz-Eakin, an economist with the center-right American Action Forum, told the Examiner. "Some may get discouraged and do the arithmetic and pay the [individual mandate] penalty."

This is the first year that uninsured taxpayers will have to pay the law's mandate penalty for not having health insurance, which went into effect in 2014 but is paid in a person's tax return. The penalty in 2014 was $95, or 1 percent of income above the $10,000 filing threshold, but goes up to $325, or 2 percent of the threshold, this year.

Len Burman of the nonpartisan Tax Policy Center said it is too soon to tell how reconciliation will affect enrollment.

"It will depend on the communication strategy that [the] administration can have to avoid these pitfalls," he said.

Levitt noted that the administration warned enrollees about reconciliation, but said it is a complicated topic. "It won't be surprising if people didn't fully understand what was happening," he said.

Reconciliation isn't the only issue facing some Obamacare customers.

The administration also accidentally sent an incorrect tax form to nearly 1 million people, which sent officials scrambling to correct. Officials asked the Obamacare customers to delay sending in their return until they got a new tax form.

The administration said last week it must get the correct form to about 1,200 people. The form is used to calculate how much subsidies a taxpayer should get based on their income.

Administration officials did not return a request for comment as of press time.