Retirement tax questions

At the time, I didn't realize I had to fill out that excess contribution form so I just took out the 1500 from the ROTH myself. I've since realized my huge mistake and gone back to them to have it corrected but since its now past the filing deadline for 2021, they cant go back and calculate earnings on that $1500. So, I figure I have to now just file it as an untimely return for 2021 and take the 6% penalty? Is this right? I haven't come across this situation on any of the forums. Right now they have corrected the 1099 R to say $1500 as my gross distribution in box 1 and in box 7 codes PJ. No other boxes are filled in.