So about 5 years ago we redid our floors with Bona HD Traffic in Satin. They came out great but I recall it took about 3-4 weeks for the floors to fully cure (some would scrape off with a fingernail)

Fast forward we moved and did our floors again. This time we used Bona Traffic HD Semi gloss instead of satin. We followed everything to a T. Sanded all the proper grits and got the floor down to perfect state to stain. We cleaned and dusted. We used Bona stain and followed instructions did not apply it heavily and did it on a relatively non humid day. Bona stated 3 hours dry time for the stain which we did, followed by mixing the two part system, shaking it as stated and allowing it to sit for roughly 8-10 min before application.

We are exactly 7 days in and I can scratch with my nail and the floor scratches. I am trying not to panic at this stage as I "think" this may have happened the first time around as well but I can find no literature stating a long cure time. I wonder if I got a bad batch but we checked the expiration and it was good.

Floors are red oak and the previous home was also red oak. If there was any type of product or residue on the floor we sanded so much off there is no way anything could have been left. Anyhow is this normal the long cure time?

I can only think that the stain was not properly cured before the finish was applied.
The conditions need to be almost perfect to be ready for a coat of finish after only 3 hours. Maybe the 3 hour dry time was to be for a poly-urethane finish instead of a two part water-based finish. You need to talk to a technical person at Bona.