Ok I found a pretty hacky solution. All you need to do is use the UIDynamics framework in some way before presenting your SKScene. For example, simply running this one line of code before presenting your scene will remove the weird physics bug caused by simultaneously using SpriteKit and UIDynamics at the same time:
UIDynamicBehavior* a = [[UIDynamicBehavior alloc] init];
I'm assuming internally this prepares the physics engine in such a way that sprite kit physics will behave normally. Unfortunately I do not trust this solution because it might not work one day and my entire game would suffer because of it.
So as an alternative to the UIDynamics framework I've decided to just use UIView Animation to replicate some of the interesting physics effects that I got with the UIDynamics Framework.
EDIT FOR IOS 8 According to doctordoder, this bug still exists in iOS 8, and this workaround still works.