Thank you all for your input. As for the question of did they put it in writing...here is a cut of the email I was sent by HR:
"Per our 2017 semi-annual 401k audit and due to an error on my behalf, you have over-contributed to your 401k plan for 2017 in the amount of $3010.78 as of 06.09.2017. Therefore, your 401k contribution withholding has been inactivated until the amount of $3010.78 has been reached. This will be calculated based upon your bi-weekly wages and your previous contribution rate of 6%. Updates will be provided every paydate via email until the over-contributed rate is reached. Your new election rate of 20% will not take effect until after the amount has been satisfied. Attached is your information as of 07.07.2017.
Should you have questions or concerns, please do not hesitate to contact me. Thank you and I apologize for any inconvenience this may cause."
So, with them handling the correction in this manner, it will take the remainder of the year for the payback and I will be unable to contribute anything more than that this year. I called her and spoke to her and was told this was how they must handle it because if they get audited they can get in trouble. I am not familiar with how the irs deals with errors made so I feel I have to accept their remedy...or at least, that is what they expect me to do.