You mentioned a rollover of after-tax money from your 401(k). Because you did not describe this after-tax money as having come from a Roth account in the 401(k), I've assumed that the after-tax funds had been in the traditional account in your 401(k).
Unless ETrade failed to follow explicit instructions to split the rollover into separate deposits into traditional and Roth IRAs, there is nothing to fix with regard to the rollover itself. The rollover deposit to the traditional IRA was permissible and is irrevocable.
If ETrade failed to follow explicit instructions to split the rollover into separate deposits into traditional and Roth IRAs, then they should be able to correct this as a bookkeeping error. If they refuse to do that, then you could have a legal dispute with ETrade.
If the rollover remains a rollover of the entire amount to a traditional IRA, it's your responsibility to track the basis in nondeductible traditional IRA contributions that your traditional IRAs acquired via the rollover. I've already explained how that adjustment to your basis in nondeductible traditional IRA contributions is to be reported.
