Yeah, try not to mix Physics with other behaviors like Platform, Bullet, 8-Direction etc. You also should only move Physics objects using Physics actions (apply force, impulse, velocity etc.), don't just change their position or angle directly.
All these things are not strictly forbidden, but if you mix physics and non-physics, the object may behave in unexpected way, interact with other objects incorrectly etc.
That being said, there is an example of physics platformer game on youtube. Nobody knows how it's done, maybe it's a clever mix of both behaviors, or the author made his own platform engine with physics. We discussed it here:
EDIT: All of the above applies to Chipmunk too.