Rotating machinery has eccentric phase differences between its components due to assembly and manufacturing errors, changing the dynamics of the system. This study investigates the effects of the phase difference between two eccentricities of rotor components on the nonlinear dynamics of the rotor in contact with the stator. The rotor composed of two disks where an eccentric phase difference exists is modeled via the finite element method. Further, the rotor physical contact with the stator is expressed using the Kelvin-Voigt and smoothed Coulomb models. The constructed model is analyzed using the brute force numerical bifurcation diagram. The analysis results show that detrimental behaviors such as the backward whirling and partial contact motions observed in a rotor-stator contact system are revealed to be more likely to occur as the eccentric phase difference between two disks decreases. These results can offer precious knowledge about nonlinear dynamic characteristics and assembly of components, resulting in the improvement of safety and production efficiency of rotating machinery.