If you are not sure why, you should ask your former landlord. Generally speaking, a late charge is not permitted in California unless expressly set forth in a lease or rental agreement. Moreover, it seems odd to have a late charge on pro-rated rent. (There aren't sufficient facts in your post indicating any basis for a late charge, even if there were a late charge provision).
Frank W. Chen has been licensed to practice law in California since 1988. The information presented here is general in nature and is not intended, nor should be construed, as legal advice for a particular case. This Avvo.com posting does not create any attorney-client relationship with the author. For specific advice about your particular situation, please consult with your own attorney.