The most common mistake is shooting on a cel phone, and most cel phones shoot at variable bit rates. There is NO good application that likes variable frame rate footage.
There are apps for phones that force their cameras into shooting fixed frame rates. You should always use such an app when you shoot.
With the problems you're having, you'll need to re-shoot if you shot on a phone. You can try to transcode the footage using an application like Handbrake (free), but you may be disappointed with the results. You may have to chalk this one up to a Hard Lesson Learned.
KGAN (CBS) & KFXA (Fox) Cedar Rapids, IA