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.