wej works just fine with the continuous. I am not yet closing windows; I am not yet in the process of closing windows.
You can, as you suggest, usually distinguish which wej it is through context. There is no context in Duolingo, so it's hard to know which wej is needed here.
wej Qorwaghmey tISoQ can mean either Don't close the windows yet! or Close three windows! You can't tell which without further context.