As of summer 2016 we are using the LAMMPS project issue tracker on GitHub for keeping track of known bugs that are non-trivial to fix. This includes discussion of how to best solve them, or explanations of temporary workarounds. LAMMPS users and developers are encouraged to submit bug reports on GitHub or to the LAMMPS mail list.
Please see issue #42 and issue #69 for examples of how to report issues.
After a bug is fixed and the corresponding issue closed, it will also typically be referenced - among other bugfixes and new features - on the Latest 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.