That's because The Times doesn't tally all purchases, and intentionally doesn't tell anyone how exactly they put their list together. Mainly, they track sales by sampling a secret selection of a few specific stores. Their list excludes purchases from stores it doesn't monitor, as well as purchases direct from the publisher, many pre-orders, and even a lot of online sales.
Other exclusions are even stranger, and we only discover them when someone pokes around. Some people thrilled with Don Jr.'s New York Times ranking were less thrilled a year earlier when a book by Jordan Peterson appeared nowhere on the list despite being the fourth-highest-selling book in America. Pressed, The Times explained that they excluded it because the publisher was headquartered in Canada.
And while publicly no one knows which stores The Times samples to compile its list, some companies absolutely know, and for a fee, they'll strategically buy your book from them. In 2011, the UCLA Health System hired one of these companies and got an otherwise obscure book on healthcare customer service to the top of the list. The week after, with no one juicing the numbers, sales dropped 96%. Doesn't matter, because their marketing will always be able to boast about it being a #1 bestseller.
So if you have an idea for a YA novel starring yourself as a girl with superpowers in a love triangle, good news! Bestseller status can be yours instantly, for a price. Just don't get caught.