As you have explained, this is simply a mistake. You are trying to fix the error by amending your 2018 taxes.
When you apply for your N-400, be honest and answer "yes" to that question and then provide a written statement and explain in full details on what happened. I would also provide a copy of amended 2018 tax returns to support your statment. Furthermore, if your CPA can provide a statement that they made a mistake, it would help to attach their statement as well (I doubt your CPA will do this). Again, mistakes happen and your are dealing with it. Good luck.
He works for you. He messed up, he's supposed to be the professional. You should be expected to tell HIM what forms to use. The least he can do is write a note. If he's not willing, he wouldn't be my CPA next year.
