"I then used Minwax Satin poly to clear the floor."

Is this a rated product for floors?

I forgot to add that your analysis is probably correct. You didn't stir the poly enough before the first coat, leaving all the flatting agent in the bottom of the can. Then the excess of flatting agent made the second coat too dull.

Yea i feel a little dumb but i was worried about creating bubbles. It wasn't until it was too late when i found out about the flatten agent. I just thought a light stir at the start would be sufficient. When I got to the bottom of the stain it was heavily coagulated as well.

With the satin varnish, once you open it, you can set it in a pan or bowl of hot tap water, it soften the flattening agent in the bottom of the can and makes it a lot easier to get it completely stirred good.

I'm worried about the "milky white" when it dried. That could be adhesion failure already lurking below the first coat. Do you have photos?

And please stay away from Minwax...it is low-end DIY stuff that has a very poor name in the professional circles (and yet so many people use it - I'm mystified).

Water based stains can have issues with Minwax...and vice verse. Minwax stains can have issues with water based finishes. And yes...Minwax has issues with bubbles that's why it is a STIR ONLY material.

Good luck. Don't do anything until you figure out the "milky white" patch. If that is adhesion failure then anything you do today will be a waste of time and money. Give it a minute and inspect that patch.