I think it just boils down to two things: the expectation by the aunt that she could just walk in, unannounced and uninvited and expect to use the OP's facilities, and then the blatant disrespect and assumption that she was ENTITLED to get the OP's house dirty just because she didn't want to take care of a common courtesy of taking off her shoes. Furthermore, she assumed that the OP should just clean up after her.
The cleanly washed floors just exacerbates the problem. It's only natural that once you give something a good cleaning, you would expect it/want it to stay as clean as possible for as long as possible. I asked my kid to clean something, and he whined 'well, how do I know that it will STAY clean? I don't want to clean it if people are just going to mess it up again.' Yes, it will get messy again....that's life. But to intentionally mess something that was JUST cleaned because you're too lazy/entitled to take necessary precautions...well, that's disrespectful and dismissive of the OP's efforts and the fact that nobody has the right to come into someone else's home, make a mess and then expect the homeowner to clean it up.
And the aunt calling the OP rude? Yeah, rude people usually deflect like that when they, themselves are the rude ones. They try to take the attention away from their own bad behavior by going on the defensive and calling someone else rude. Exactly what the aunt did.
You're fine, OP. And no way would I be apologizing to the aunt. In fact, if it was brought up to me again, I would go all outraged on her and tell her that in YOUR house, NOBODY gets to intentionally make a mess and then expect someone else to clean it up (asserting your independence as an adult here), let alone someone who doesn't even live there, which is what she told you to do. And (said with a sweet smile) in the future, please call first before just dropping by unannounced to make sure that you're up for visitors.