Why do I still have a balance when Checks from Insurance Loss Claim, Warranty refund and Gap Insurance received?

I bought the care in December 2015, January and February loan payments were made on time on March 3, 2016 the vehicle was hit and totaled. Payoff quoted $16,623.15 Insurance Settlement $11,602.88 applied on April 07, 2016. Warranty Refund $1,786.67 July 15, 2016 and Gap paid $3,233.60 August 12, 2016. I still have a balance accruing because the payments were applied but not back to the date of Loss. Can they do that?