Tell people about upstream problems and possible workarounds
As package providers it is our interest to give users the best possible experience. Yet sometimes there are problems with trajectories, topologies or upstream packages we don't have complete control over.
It might be helpful to have a section at the very top of a module documentation that states problems we know about but are 'wontfix' and propose a possible solution.
The most recent example: Module: Epsilon Problem: Simulation with virtual sites, but not saved in the trajectory (LAMMPS and TIP4P water). Solution: Simple loop over the water residues, shift the atom to the position of the virtual site. (Example code for TIP4P* waters could be given)