I doubt you are going to find technical information on what is the "correct" way to model simple-span beams. For a simple shear connection the members should be modeled to (ideally) only transfer vertical shear. However, in order to eliminate irrelevant errors and "zero stiffness" warnings, modelers will sometimes choose to "fix" the weak axis and torsional moments at some, or all beam ends in the model. Although this method can be risky from an error-catching standpoint, so long as the members are not loaded in such a way to induce torsional or weak axis moment at the member ends, the model may in fact be fine.
The easiest way to check whether the model is handling the loads in the assumed manner is to print member end forces (or turn on the member force diagrams in the GUI) and see if any members are picking up (or delivering) unintended load to other members. If they are, then this is your justification to the other engineer (ex. Beam XXX looks like it is currently transferring significant torsion to column XX, did you intend to release My for that member or are you planning on somehow transferring that force through the connection..) That should go over a little better than a blanket statement on mow member ends are supposed to be modeled.
At the end of the day it does not matter so much just how it is modeled so long as there are simple clear load paths and connections to resist the applied forces, and the model matches the detailing in the drawings.
Regarding the "instabilities" do a search of Bentley's forums and help files. In many cases this is actually a member that is technically able to rotate about some axis but may not be loaded in a way that induces the rotation (i.e. a simple span beam loaded in the vertical direction with Mx released on both ends will give a instability warning due to the fact that it is modeled like it is free to twist - While this is technically correct, the minimal torsional resistance from a standard shear connection is adequate to maintain stability so long as there are no loads that induce torsion.)