If there was a mistake the IRS may correct it and amend your return for you. If they do, they will send a letter explaining what they did and why. It might be the case where you do owe taxes even though they took taxes out on the 1099-R distribution, it might not have been enough. When they withhold taxes they calculate generally around 20-22% taxes withheld, but they do not take into consideration your entire tax situation, so if there are more income and retirement distributions on the total you might not have had enough withheld.