TL;DR - She cheated on the King.

Slightly longer version: it could be proven in a court of law that Catherine had been unfaithful. There were witnesses that could be presented who could testify they had arranged for her to meet with her lover. We also know she was unfaithful because before her execution, she proudly declared her undying devotion to her lover.

You might think "but the king had been unfaithful to his various queens!" Yes, here was a double standard. The king's wife was expected to be accommodating to him alone and chaste otherwise.

One must also remember that in those days, her "queenly duty" was to get pregnant with an heir to the throne. If she was cheating on him, the child's parentage would be in question, and that could throw the line of succession into chaos.

So cheating on the King wasn't just considered adultery, it was considered treason.