The homestead exemption is your responsibility. You should have filed and should file for next year as soon as possible. What county do you live in? Many have the ability to file online.
If at all possible you should attempt to do your own escrow. Florida is one of those states where you are better off doing it yourself. You should talk to the mortgage company and see if there is any possible way to do your own escrow.
I'll explain more later.
You will have lost money on one years property tax exemption. If you live in Orange county it would amount to about $420, if you live in Palm Beach county, about $515. Its not the end of the world and yes that money is lost. Given that Palm Beach county has some of the highest millage rates, the estimated taxes were off by quite a bit. For reference you can look up the tax history of the property on the appraisers web site for your county.
The exemption is 25K, so you multiply your county's millage rate by 25 to see the value of the exemption.
While escrow increases are a pain short term, you will not lose any excess money paid into escrow. Eventually your escrow payment will be reduced to reflect what is actually owed.
My last escrow experience was in 1999, so its been a while. I found the company I dealt with had outdated software and the CSR did exactly what the computer told them to do. They could initiate an inquiry but were unable to provide any intelligent analysis to the situation.
Here is why I would do away with escrow in Florida:
In Florida property taxes are due on March 31. However, if you pay them in November you get a 4% discount, 3% in December, 2% in January and 1% in February. Guess when your escrow agent will pay the taxes? In March. It won't matter if you have enough in your escrow account.
For perspective, my discount was about $150 on the two properties I own. Not all that significant if you miss out on this for a year or two.
So dummy me called up the escrow company and insisted that they pay the taxes in November to take advantage of the full discount. There was more than enough in the account. They did. Come December the computer sees that my property taxes are due in March and I don't have much left in the account. It did not consider it wasn't until March of next year. That December my escrow payment went up by $800. My mortgage payment almost doubled.
If you are disciplined to save, just do it on your own. In order to do so you will need to have 20% equity in your home.