Retirement tax questions

I'm in this same situation right now, but my 401k is a ROTH. I'm guessing that I won't be taxed on the return of excess because it was already taxed. TurboTax says to fill out the 1099-R but Fidelity won't send one until next year (which seems "normal"). The instructions aren't clear on how to fill out this form for a traditional vs roth 401k, and I don't want to be taxed on the excess since it was already taxed when going in... any advice?

Also, I overcontributed $4163 and my refund from my 401k plan was $3876, so I'm assuming it's because of a loss in the market between contribution time and refund time. I'm concerned that when I enter the actual refunded amount of $3876, it won't match the overage of $4163 and that will be a red flag?