Thanks! I found out what the problem was. If a node inherits from CCNode and tries to define a physics body without using the property but directly through the ivar _physicsBody, it would result in _physicsBody.node not being set. When the ccPhysicsCollisionBegin is called, the parameters are nil even though the Chipmunk bodies are there.
To avoid this, one must assign a physics body through the property instead of the ivar (which should be private).
You can check out the original thread from the Cocos2d-iphone forum here: http://forum.cocos2d-iphone.org/t/cocos2d-3-0-physics-collision-begin-selector-called-with-nil-parameters/13316