Skyler you asked me a few questions earlier about the fees, discounts, refunds of fees, etc. It is hard for me to answer those questions, because each firm has different policicies. Our firm's policy is to pay for any interest or penalties associated with our mistake and fix the problem without additional charge. The taxpayer is responsible for the taxes owing as that would have been the case if we did not make an error. As I mentioned our minimum is like $1,000 with a typically return costing $2k - $3k and larger returns costing $20k+ for an individual. What you get is someone preparing the return, an experienced person reviewing the return, then a partner level person reviewing the return and signing the return. If there are complexities, then experts in those areas would also review certain components of the return. This multiple review process catches most issues, before it goes out the door. With that being said, we still have instances where we drop the ball. That is when we appologize, fix the problem, and pay any penalties or interets that are incurred because of our issue.
I look at this approach very similar to any other professional service. I have not been offered a discount from doctors, lawyers, plumbers, mechanics, etc. if the work that they performed did not fix the problem. I have had them redo something at no additional cost, which I was happy about. Typically, those other providers would charge you extra to solve the problem. So I would think your current CPA was fine on the billing side, it sounds like the appology was lacking.
CPA fees are deductible as a business expense. In some cases, preparers allocate some small amount as a personal expense and the rest as a business expense. I would also say that there would be a case to expense Turbotax or anything else that was needed to run your business as an expense.
If you choose to prepare your own tax return, you will learn a lot, you can ask for advice from those on the board, and there are lots of other resources. Turbotax, the IRS, and others are typically not fully ready to finalize a tax return before year-end and depending on the last minute tax law changes they sometimes don't have the systems in place to finalize before mid to late January.
If you are going to stick with a CPA, which I recommend for complex tax returns, then I would check on credentials. I would ensure that they have a multiple stage review process, and that they are as aggressive or conservative as you feel comfortable. Typically, those who are charging very little are being prepared by a sole owner who is working 80-100 hours per week. They can be brilliant, but still make mistakes based on no review and fatigue.
Good luck!
P.S. I do a very narrow tax incentive for corporations, so I am worthless to friends and family. The wife is not always sure that I should be preparing our own return:) I have prepared a few thousand individual returns over my career so I understand how a tax return works, but the rules and the software tends to be the hardest hurdles to overcome each year.