It seems like the problem is that if you use the snipping tool to save to a file that already exists it only modifies as much of the file as is required so that

It seems like the problem is that if you use the snipping tool to save to a file that already exists it only modifies as much of the file as is required so that the new image you saved is visible - the rest of the file's data is preserved. The problem is saving to a file with more information than the cropped information requires - the original images information "overflow" isn't removed. So if you're saving to a new file it's fine, there's no extra information.