The original fees charged by a bankruptcy attorney usually cover all the work up to confirmation of the chapter 13 Plan. After plan confirmation, any work done extra would result in additional attorney's fees, to be charged on an hourly basis. All of this should have been spelled out in the retainer.
I am in the 7th Circuit, so I can't say the rules are the same in your jurisdiction but here we are allowed $4000 in fees without petitioning the court for additional fees. I usually collect $800-1000 up front and put the rest in the plan. Once the plan is filed, I CANNOT charge my client additional fees. Once the case is confirmed, I get paid the balance through the Chapter 13 plan. I also must represent my client to my fullest as a condition to the entitlement to those fees.
Regarding your question with mortgage fees, the mortgage company is allowed to pass onto you "all costs of collection", which includes attorney fees related to bankruptcy. However, to file a Proof of Claim attorney fees shouldn't exceed $200. If you fall behind and they file a Motion to Lifty Stay, plan on another $800 in fees. If the error was on their part, I would object to the attorney fees. The only way I could fathom $2500 in fees is if your house was in foreclosure and nearing Sheriff Sale when the case was filed. Even then, in our jurisdiction the mortgage company must attach to their Proof of Claim a break down supporting their claim.
Call the U.S. Trustee's office in Portland -- (207) 780-3564 -- to complain about your attorney, but don't go into great detail about the mortgage problem unless they ask. I think your attorney probably has a duty to represent you and may actually have to give you some money back.