TurboTax treats a code-3 distribution received before normal retirement age as being ineligible for rollover. TurboTax therefore ignores any indication by you that you did a rollover. It's unusual for a payer to use code 3 for anything but a disability pension (which generally is ineligible for rollover) because the payer normally does not want to be involved in determining your disability status except in the case of a disability pension.
Regarding the indirect rollover back to the same account, something doesn't seem right about what was said. An indirect rollover is required to be reported on Form 1099-R because during an indirect rollover the funds come under your control. It's only your actions after a reportable distribution has been made (the rollover) that makes the distribution nontaxable. It's possible that, if funds were distributed in error, the plan might pretend the distribution never happened if they take back the erroneous distribution.
