If the check was made out to the new IRA (in this case, the SEP IRA, and is sounds like it was, or was at least made out to the new IRA custodian for your benefit), this was a trustee-to-trustee transfer of the IRA and there would be no Form 1099-R; trustee-to-trustee transfers are not reportable on either Form 1099-R or Form 5498. However, if the check was made out to the IRA participant, it is required to have been reported on Form 1099-R and reported on the participant's tax return, in this case as having been rolled over.
If no Form 1099-R was issued by the old IRA custodian, apparently the old custodian considered it to be a trustee-to-trustee transfer. However, it seems that it was incorrectly recorded at the new IRA custodian, resulting in the issuance of the Form 1099-R. If the Form 5498 shows it in box 2 as a rollover contribution, the IRS might question the transaction without a corresponding Form 1099-R showing a distribution, so be prepared to provide explanation that this was actually a trustee-to-trustee transfer of an IRA, not a distribution and rollover. If the amount is shown in box 1 as a regular contribution, that's probably a bigger problem, and you should request a corrected Form 5498. Even if reported as a rollover contribution, if the movement of the IRA was done by a proper trustee-to-trustee transfer, it wouldn't hurt to request that the receiving IRA custodian correct the Form 5498 to show that no regular or rollover contribution occurred.
And to answer your original question, you should answer No when TurboTax asks if this was a contribution.
