Update:
3 weeks after messing up my 2 paychecks, my company deposited the missing employer match as QNEC in my 401k account. At first the Benefits Team sent me an email template about missing pre tax contribution but nothing about after tax contribution. So I had to follow up with them again. I guess only a tiny portion of people make after tax contribution and the Benefits are not familiar with it at all. Then they sent me another template, basically saying "Oops we messed up but too bad. We are sorry but nothing we can do. We will NOT lift 50% after tax contribution limit and you CANNOT make up these 2 missed after tax contributions. You can increase your pre tax % or contribute to roth 401k." Excuse me?! Pre tax or Roth 401k are different animals, ok?!
To answer your questions -
Yes, I am contributing to after tax 401k (not Roth 401k) and doing in-plan conversion to my Roth IRA.
And yes, instead of "pretty sure", I am 200% sure that I am nowhere near any IRS limit (pre tax $18000, pre tax + roth + after tax + employer match $54000). My contributions have been working for several pay cycles but suddenly something went wrong...
One more question -
Should I say "ok. thank you." to my Benefits Team and let it go? Or send IRS link to them and say "Not done yet. You guys owe me 40%"?
Thank you!