When there is a pump and dump, some manipulation, that means trading, they trade to manipulate, and when they trade, they leave trading fee, which makes money for the exchange. This is why many exchanges allow it to happen and that's a bad thing to have for an exchange but more money so they accept it and let it happen.
The exchange do it too because of this same reason as they want to create a buzz around certain projects to bring in traders that'll buy and sell the coins and make them money. The exchanges don't mine if you're winning or losing because despite anyone that you get, you'll be making them money always, this makes them the winner always.
Market manipulation happens more frequently than we think because some of the profits we received are done intentionally by the exchange because you'll now fall for their next tricks when you make a profits from your initial participation. Exchange sometimes take money from some of the projects to make them more popular on their exchange and this can make them to do anything possible to give the project that popularity.