Kat,
You have the Moultrie 990i as mentioned in your first post, correct?
I did a quick search and see it takes pictures (JPG files), videos (AVI), and a special MLT file which is used by the software that comes with the camera.
Bob and the others know more about this than me. I have a couple cameras with SD cards. When I connect the camera directly to a computer it sees a certain file folder hierarchy. If I plug the SD card directly in the computer, the file structure is significantly different. I suspect the computer sees the camera as an ordinary USB drive, and the SD card as a different kind of storage device. No matter, the computer hasn't damaged any card using any method.
I have plugged both into my iPad 3 using the Apple Camera Connection kit, and all kinds of weird things happen. Some times it transfers all the pictures and other times the iPad is more confused than me. Anyway, I have quit using the iPad for anything photo or video related, other than transferring files via syncing in the default folders on my computer, which is running MS windows. Through all of this neither the computer or iPad did anything to change the SD card itself.