It sounds like you are entering the rollover as an IRA contribution under Deductions and Credits. A rollover is not treated like a contribution, and is not entered within the contribution section. Please back out any dollar amounts you entered here that don't represent "new money". New money counts towards an IRA contribution, not money coming from a 401(k).
You account for your rollover within the income section. You enter the 1099-R, and indicate that it was rolled into an IRA.
You wouldn't receive excess contribution messages if you only entered a 1099-R. Please review the entries under Deductions and Credits- IRA contributions.
