You may have a serious problem.
How old are you? How much did you rollover? How much taxes were withheld? When was the date of the rollover?
Here's the problem. Suppose you rolled over $10,000 to an IRA and the 401k plan withheld $1000 for taxes. That means the IRA only got $9000. That means only $9000 was a rollover, and $1000 was a taxable withdrawal. (You "kept" the money–even though it was credited to your account at the IRS, it counts as if you kept it.). If you are under age 59-1/2 (or under age 55 when you left the company) you also pay a 10% penalty on the amount that was kept out of the rollover.
There may be a way to "top off" the IRA to make the rollover complete. But I think that deadline is already past.
That means you will pay some tax and maybe penalties. When you enter the 1099-R for the distribution (let's say $10,000) and the program asks what did you do with the money, you must say you rolled over part of the money, and give the amount that was actually deposited in the IRA. The rest counts as a taxable withdrawal.
The 401k plan should not have withheld anything if this was a direct rollover from the plan to a traditional IRA.
