As mentioned above, the mulliken charge analysis cannot represent exact charge populations on certain molecule. Just try to analyze another options (NBO or Hirshfeld)
Mullikan charges are only mathematical abstracts that do not represent the exact experimental charges. Using other methods like NBO with advanced basis sets can give charges that match the experiment.
Mulliken populations do not have any physical meaning, because they have no mathematical limit as the basis set is improved towards completeness. Hirshfeld method yields atomic charges that are usually too low in magnitude. For a better approach, see the DDEC6 method introduced in these papers: http://dx.doi.org/10.1039/c7ra07400j (open access), http://dx.doi.org/10.1039/c6ra04656h, http://dx.doi.org/10.1039/c6ra05507a