If bones affected by a constraint are in a skin but the constraint is not, then you will get the warning. This is true for all types of constraints, not just physics constraints. This is because the constraint cannot be applied when the bone's skin is not active. To fix it, add the constraint to the same skin as the bones.
If your physics constraint has rotate, scaleX, or shearX > 0 and the bone length is 0, then you will get the warning. The physics constraint cannot apply those to a 0 length bone.
If your physics constraint has x, y, rotate, scaleX, and shearX all set to 0, then you will get the warning. This is because the physics constraint would do nothing.
In the near future we will add text to explain the warnings when they appear.