Are you sure the other guy has the app or can even get the app on his device?
I had this same issue but instead of me no being leader it made me the leader and I can't run the app on my phone until I get my upgrade in 2 months. None the less my friend is not very happy about this whole thing.
It's pretty dumb to make one major part of game be controlled from a completely different application.
So now we have a FPS which unless you have a good phone or tablet you are screwed out of clan management.
I'm a programmer and you know it was just plain wrong thinking on this move.
The only suggestion I can think of is to get the other guy to leave the clan via the console (Barracks -> Clan Details -> Roster -> Click on own name -> Leave Clan) which MIGHT, not even sure this will work, then transfer you to Commander at which point you should be able to invite them back into the clan. I haven't looked but there may even be an option for them to transfer Command role to someone else in the roster.