Accidently deposited after tax 401k check into checking account....before rolling over into IRA

My wife left her company after 15 years.  She had approx. $75k in her 401k.  We assumed it was all pretax.  However, when talking to the financial institution, they informed her that $50k was pretax, and $25k was after tax. 

 

The $50k pretax was sent in a check to Fidelity which we deposited in a 401k.

 

My Questions:

 

1) The $25k after tax check was made out to her.  I think I made a mistake to advise her to get the check made out to her.  She is not 591/2 and will perhaps have to pay the 10% penalty (there should be no tax as this was already after tax....I think).  Will we have to pay the 10% penalty....but no tax?

2) Since this check was deposited into her checking account, does that NOT allow for the $25k to be rolled over into a new Roth IRA (direct or indirect, or a Mega-Backdoor Roth contribution) and thus avoid the penalty?

3) Any other options?