I just finished applying my first coat of finish on my hardwood flooring. I used Minwax's water based polycrylic, and just saw the part stating that it was not recommended for flooring. Will I be alright finishing with 2-3 coats of a water-based polyurethane over it, or will I need to remove the polycrylic and start over. If I do need to start over. What is the best way to remove the polycrylic? Thank you in advance.

The first coat is a seal coat. It shows the color and becomes a base for more coats of finish. I think that it would be fine to keep the coat that you used without sanding to bare wood. There could be an adhesion problem, so you could ask the Minwax people what they recommend. My experience with some poly-acrylic finish is that it gums sandpaper so it is trouble to sand completely to bare wood.