CHFA Incompetence at its highest, misuse of funds Lake Zurich Illinois

I am a new homeowner (6 months) and take pride in this by paying my bills on time. Our mortgage started with Cornerstone and then went to CHFA. I have had numerous issues with CHFA and misuse of checks that have been applied to the wrong accounts.

I have two mortgages, but my second mortgage is only $28.41 yet my house payment of almost $1400 was applied to this mortgage even though that account is on auto draft. I was not receiving statements for my house payment so put two account numbers on my check and on a letter I enclosed with my check. Well rather than using a little common sense they applied the check to the wrong account. Why would I pay over $1000 to an account I only owe $28.41 on and then not pay my mortage? I received a collections call this evening which is how I determined the problem. 

I also had issues with checks being cleared and then CHFA calling me to say I hadn't paid even though I had proof from my bank that no check was bounced and all had cleared. It is soon to refinance or I would just to get a different mortage company.