I have been struggling with this problem for a while, if you select a Zoom input as a source for a layer of another input, you can't do any cropping on that layer. Positioning and even rotation works, but not cropping. But I just figured out that if you apply a key mask to the Zoom input itself, even if it's an all white mask that has no practical effect on the Zoom input, suddenly you can crop layers that use that Zoom input! Hopefully this saves some others the frustration I was dealing with

Yeah I don't know...if I make a new input and put a zoom input on a layer I can crop it fine, but with my inputs that I built and populated layers with inputs some Zoom and some not, I couldn't crop. If I figure anything out I'll let you know, thanks!