Some of these cases are not only dark patterns, they constitute was it legally known as fraud. If you deceive someone in order to gain a financial advantage, it is fraud. The problem is that going against those gigantic companies is very difficult.
The article says that they imply "cheapest at the top". No, the flights aren't shown "cheapest at the top", and they never imply they are. They're sorted in chronological order.
There is a summary item that says the lowest fare for a booking class that day, but that's all.
That sentence makes it sound like they deliberately always put the 2nd lowest price as the lowest every time. It was pretty misleading or poorly written.
If I saw those boxes across the board, like in their example image, it doesn't take a second thought, it's "obvious" (to me anyway), that those are the "lowest, per class".