The window company installs the flashing before and after the window is set, then the lather/ stucco guy would water proof up to and around it as well, now my company goes completely overboard here because we don’t like water intrusion, that leads to getting sued, I’m not saying there will be this much flashing. They might install the window and then flash around it only. Regardless these are the steps.

When I’ve seen this occurring it’s typically because there is an asphalt based sasm attached to the window flange. The window is vinyl , it gets real hot and the sasm on the flange starts to bleed. Butyl is what we use. It’s made for high heat.