The other day I was working in Affinity Publisher, planning to make my text flow around a photo. But Pixelmator Pro, 2.0, does not seem to be able to export in the PSD format, at least not when we are talking about cropped images...
The image shows what it looks like when the image is opened in Photoshop.
Have you been cropping with the Hide mode turned on, by any chance? This mode crops images nondestructively, hiding the cropped image areas beyond the edges of the canvas. Switching to the Delete mode should help.