There is bug in iPadOS15/16 that impacts markup/cropping of screenshots and Photos. This particular bug has been resolved in iPadOS 17.x.
For those users who have not yet updated from affected versions of iPadOS, there is a workaround...
First - save the cropped and/or marked-up image - at which point, when reviewed, the markup appears to have been lost. Saving another screenshot/image will make edits made to the previously saved image visible.
Interestingly, if an initial screenshot is triggered using the corner-swipe gesture with an Apple Pencil, the markup usually saves without needing to trigger a subsequent screenshot. If not already configured, you can configure the corner-swipe as follows:
Settings > General > Gestures >
- Allow Finger Swipe from Corner - set to OFF if you only wish to use the Pencil and not your finger
- Left | Right Corner Swipe - select Screenshot for one, other or both gestures
Now that you have enabled the corner swipe, you can easily capture a screenshot with just your finger or Apple Pencil). Just swipe diagonally from the lower-left or lower-right corner of the screen towards the centre; this will immediately trigger the screenshot.