Patent Agreement in Order to Graduate

Yes, it is normal. Universities often require this - especially of faculty, but also, often enough of students.

You have an issue that you can probably work out with the university. If the patent wasn't related to your work in the educational program, then the university probably has no real claim. But the lawyers for your employer and for your university should probably both be informed of the situation and have a chance to discuss it.

But given your statement that it has nothing to do with the university, I would expect you to get a waiver. Or perhaps just a modified document exempting that one project or (better) making it clearer that it only applies to patents that were, in some way, supported by the university.

But I wouldn't make assumptions and I wouldn't sign the document without advice of a lawyer.

My first question is, is [being told to retrospectively assign patent rights] normal?

No: Assigning any patent rights in advance is normal, doing so retrospectively is not.

My second question is, I did file a patent during my enrollment, however, it was with my employer and had nothing to do with my school work, will this cause some sort of conflict of interest?

No: The school seemingly have no rights, presumably your employer does. Note that retrospectively assigning rights to your school will create a problem, moreover, you could be personally liable (e.g., if you assigned rights to two parties).

If you filed a patent having nothing to do with the university, and then sign a paper saying that the university is the assignee for any patents you filed with the university during your time there, OF COURSE there is a possibility that one impacts the other. You may be ceding exclusive ownership on behalf of your employer -- and there have been cases where such things have been upheld in court (see https://en.wikipedia.org/wiki/Stanford_University_v._Roche_Molecular_Systems,_Inc.)

If it's valuable and important, you need to be careful, and being careful means hiring a lawyer. You should certainly not sign anything that every other student has not been asked to sign.