On this project, we knew that there were several layers of flooring -- we could see evidence of the top few layers after removing a floor heat register. We did not know, however, that there was a total of 7 layers over the original subfloor. Starting from the top, you'll see in the photo: vinyl, 1/4" underlayment, vinyl, 3/4" particleboard, vinyl, MDF, fir.
Remodeling always reveals things that you just can't see before you start tearing things apart (also known as unforeseen conditions). And, those typically mean additional cost during construction.
In addition to your known/budgeted project costs, you should have money set aside to deal with these situations when they occur. As a general rule-of-thumb, that amount should be at least 10% of the project's construction cost. And, the smaller the project, the larger your contingency fund should be.