There are two kinds of forces: conservative forces, which have potential energy associated with them, and non-conservative forces, which don't.
There are also two versions of the work-energy theorem. The first one, W = ΔK, says that the net work done by all forces (both conservative and non-conservative) on an object equals the change in the object's kinetic energy. Potential energy isn't mentioned here at all.
The second version, Wnc = ΔE = ΔK + ΔU, says that the net work done by all non-conservative forces equals the change in the object's mechanical energy (kinetic plus potential). In effect, the work done by the conservative forces has been moved over to the other side of the equation and relabeled as the change in potential energy.