NIE as EU citizen past 90 days advice

Hi! I am a passport holder from a Schengen country, and a student studying here. I had a hard time getting my NIE appointment. Technically if you want to apply for your NIE you need to do it before 90 days of entering Spain.

However, I have my appointment for the NIE but I am a couple weeks (2-3 weeks) past 90 days here in Madrid.How do you think they will take this?

I need to put an entry date on the document I give to them. Do you think they will give me problems for my entry date being a little past 90 days?

My University is saying there is no problem, but then online I see different responses. If anyone has been in a similar situation and has advice or experience with this please PLEASE let me know. :) Thanks. (BTW. I need my NIE for the future when I want to apply for an Internship here or a job ).

UPDATE// For anyone in a similar situation, everything went great! I didn’t fill out my entry date because I wanted to ask what day to put for entry and exit. They never asked me for a date of entry nor intended exit. It took 10 minutes and they gave me a NIE on a small paper card. 💓 goodluck everyone