I noticed this when I was using cropped photos in Skitch. It would open the photo in its Pre-cropped state. I thought I was seeing things, or didn't crop, even though I knew I did.
I did as I think I read above. Cropped and then took a screenshot. If you are going to use Skitch on a cropped photo: crop, select that photo, take a screenshot and use the screenshot for the Skitch. If you do not do that, the uncropped photo will have the Skitch markups. You can always crop after Skitch.
If you want an actual cropped version, do a screenshot or email it to yourself after cropping. Or, you can spend money in an app. I don't want to spend the money or have more apps cluttering my las or phone. Screenshots are quick. I prefer not to email and have the emails of photos I have cropped filling my email boxes and going through the hassle of cleaning them out and deleting. Also have no patience waiting for the darn thing to be sent and received and downloaded.
It is seems so strange to me that when you are finished cropping and you save it, you really aren't saving a cropped version.