The iPhone is a bit messed up. Originally you had to press the big button to take a photo and, I guess for right-handed people, it was expected this would be on the right-hand side. Now the iPhone allows you to use the volume buttons as a shutter button, but this has the phone the other way up and, I guess for compatibility, but to my mind inexplicably, the iPhone stores all video or photos so taken as upside down, with metadata to say its 180 deg rotated! isoftware and some other tools like Adobe Photoshop/Premiere handle this fine, but viewers that are not "metadata aware", like Windows Explorer and WMP and, probably, MC will show them upside down!
I don't know this is the OP's problem, but it's possible.