How did it show up on your 1040 return? What plan was it in? If it was from a 401k or employer plan it should be on 1040 line 5a and not included in 5b with the word Rollover by 5b. If it was from an IRA it should be on line 4a and not in 4b. Maybe it showed up on the wrong line so they think you missed reporting it.
As yes, many people have rollovers, very common. Even if you did an indirect rollover and you got the money and deposited it into the new IRA yourself. That shouldn't cause a problem.
