Indium keep rendering the "original" block models while Physics Model adds "new".
It looks like you have two blocks one over the other.
E.G. When you open a door, the default model and behaviour happens, but also the Physics Mod model and behavior.

Which version of Physics Mod are you using? 3.0.4 added support for Sodium 0.4.11.

Please downgrade to Sodium 0.4.10 and Indium 1.0.15.