Online check-in isn't a full check-in, depending on the hotel. More like a preregistration. Or when you online check-in at an airline and they tell you that you still have to finish the process at the airport.

Too late for you, but in this situation, doing the online check-in via the app is good, but then you should have used the chat feature to communicate that you were being delayed and you wanted to keep your full reservation still (you could call too, but chatting gives you a paper trail). I totally get how they describe the service and what you expected didn't match up, but that would have probably fixed the problem before it happened.

Not exactly the same, but I had a boss once that had to fly back to the office early. When we get the master bill, all of his nights are still on the invoice; no early check out. I contact the hotel and they say he didn't check out early. I question my boss and he tells me that he went to the front desk, left his key on the counter, and then walked away. I said, "did you talk to anyone?" He said, no. I explained that a key just left on the counter could be someone just returning a key that was lost on the ground, the front desk staff has no way to tell that the intent is to checkout. The hotel eventually waived the charges, but the point is, always confirm odd activities (early checkout, late arrival, etc) with a human.