There are lots of possible causes:
- typos in the input or mistakes in converting values
- too short a simulation to get converged data
- inconsistent use of force field settings
- bad geometry
- unsuitable reference data (you need to compare to simulation data using the exact same setup, settings, and force field).
Neither of those are LAMMPS specific.
Please also see About the estimation of the error in the calculation of thermal conductivity by the Green-Kubo method - #2 by Germain