I'll tell you a story about Booking.com. I booked an ostensibly available hotel in Ouray, CO in fairly peak season. I got there and they of course, had already sold the booking beforehand and because the systems didn't link up correctly Booking's availability was not updated. It was the hotel's fault, but it didn't matter. Not a single other hotel in Ouray had availability, and, if you happen to know the area, anything that resembles a hotel outside of Ouray is going to be a significantly long drive.
Booking.com was zero help at all when I called them. None. They couldn't find or book me another hotel, and basically just told me that there was nothing they could do besides refund my money.
There are many, many stories like this.
Don't get me wrong, I actually like Booking. I think it's a great way for smaller properties to get visibility without having to build and maintain that web presence themselves. But when it goes wrong, don't expect them to go to bat for you. They are incentivized to keep making money, and threatening to delist hotels for fucking over customers when the hotel clearly messed up is clearly not a game they have decided to play.
I always book directly with the hotel if I can, because, if you do that, the shit that I mentioned just doesn't happen. Sure, if it's double the price, I'll roll the dice with Booking. But it basically never is. If it's something like 5-10% of the nightly price extra, I'll pay that premium to not have to deal with any BS. Usually it's the exact same price anyway, if it's an available option (there are some hotels that literally only survive via Booking these days).