The behaviour of the bolt crossing the joint is a complicated problem and it depends on the stiffness characteristics of the joint and several bolt factors such as: the diameter of the bolt and the hole, the steel stiffness, the extension of the bolt, and the strengths of the rock and grout.
RS2 assumes that there is a relatively large axial resistance and shear resistance at the intersection point between the bolt and the joint. The external force that you applied in the model will be carried out by both the axial (tensile) and shear resistance of the bolt. Therefore, due to the combined resistance, the load capacity that you will obtain will be higher than the shear resistance of the bolt. In general, refining the mesh in areas of bolt/joint interaction will lead to more accurate results.
The Bolt-Joint Interaction document in the Theory section of the RS2 online help provides a more detailed discussion of the topic.