Yes, if you make enough income where you’re required to file a tax return, legally this is a problem and it is a criminal offense. The IRS can come after you and the longer you wait to file a return, the more criminal exposure you have. You should contact a tax lawyer and accountant and have your returns filed for 2019 asap. You’re not quite that late yet and will only pay a nominal penalty. Ultimately if you don’t file, they can place a lien on your property.
As for FAFSA, if you’re the one trying to fill it out, your tax return is also required and if your kid attends a school requiring the CSS then that’s a whole other issue and tax returns are required there as well as they need to be uploaded for both the FAFSA and CSS. They can be manually updated or the IRS tool can be used to connect and download them.
Also, the fact that you’re legally separated, if your spouse ever decides to try to get more money, or actually file for divorce, his/her lawyer will want your tax returns and if you can’t produce them at that time, you’ll be in bigger doodoo than you are now. Again, file them asap and pay whatever penalty you have to pay. While you’re still legally married there may be issues related to that as well and your spouse might be on the hook as well.