Yes, for a thermal spectrum reactor, the buildup of xenon will quickly decrease keff when depleting. As far as the negative number densities, note that the values are very low (on the order of 1e-20 atom/b-cm) and are effectively zero. Some things you may want to consider that could cause this:
- Is your power specified in the correct units? (OpenMC expects W, not MW or something else)
- Timestep lengths that are too long can also cause issues, but that shouldn’t be a problem in your case where the steps are quite short.