Retirement tax questions

Hello, just to clarify, the distribution from my Roth 401k was two checks, first check was a proceeds check and rolled directly to the Roth IRA. The second check, which apparently was my company's pre-tax match check. this check was supposedly "lost" for two months, so i had them send it to me. then I mistakenly deposited into the Roth IRA. 

My understanding is i need to pay taxes on this 12K deposit mistake. which is fine, i will simply increase my federal & state withholding to cover the estimated taxes. I just want to make sure there is no penalty that needs to be address for exceeding the yearly contribution or is this still a legal transfer?  or, should i withdraw the excess payment from the Roth IRA?