This page lists known issues and bugs in LAMMPS that have not yet been fixed. Typically this is because the fix is non-trivial and/or the bug is obscure enough it shouldn't cause most people problems. Once the issue is resolved it will disappear from this page and appear as a patch on the New features/Bug fixes page.
The following quote seems apropos:
As we know, there are known knowns. There are things we know we know. We also know there are known unknowns. That is to say, we know there are some things we do not know. But there are also unknown unknowns, the ones we don't know. -- Donald Rumsfeld
This page lists unknown bugs in LAMMPS.
The pressure computed when SHAKE and rRESPA are used together is incorrect. For NVE and NVT dynamics this is a diagnostic output. For NPT dynamics this will lead to incorrect box volumes and densities. LAMMPS will issue a warning in both cases.
Using non-Coulombic tabulated potentials via pair_style table under pair_style hybrid with other Coulombic potentials and a long-range Kspace solver (PPPM or Ewald) can cause LAMMPS to generate an error if the cutoffs of all the potentials are not the same, even when it should be OK. This is b/c LAMMPS requires all Coulombic potentials to have the same cutoff and isn't recognizing that the tabulated potentials aren't Coulombic.