Situation - Beam is deeper than the joist and you need it to be flush with the top of the joist.
Right-click the beam: Beam/Post > Set Beam Elevation.
Click a joist and click OK. The beam will be justified in relation to the joist. The warning about a linkable object just means that changing the joist elevation (floor container) will not automatically adjust the beam elevation.
The beam is justified, but above.
In the beam property grid, set the beam justification to below.
The top of the beam will be set to the top of the joist.