Issue with Crop Tool

I'm not sure if I'm doing it right or if I'm misunderstanding how it works, but I can't get the Crop Tool to work properly. I've added a Reticulation filter to a texture I'm trying to make. It's been scaled outwards, but I need everything that can't be seen on the canvas to go, otherwise it takes my file size up greatly! I've tried using the Rectangular Marquee Tool to select the part that's on show, gone to Image, and selected Crop. However, if I deselect everything, press Ctrl + T, it still shows the huge Transform box where I've scaled, which means it doesn't look as though the selection was cropped. What am I doing wrong?

Thanks