I have filed my own taxes for many years and was self-employed for many of those years. I use Turbotax and I can tell you that I've had to read and re-read questions/instructions in Turbotax to avoid making mistakes as you have. Turbotax won't stop you from making mistakes. It will flag things sometimes but you assumed that it is error-proof and it isn't. also, telling an IRS representative that it is Turbotax's fault won't cut it with them. You are responsible for your tax returns regardless of what tools are used to prepare your retun or who prepared them.
If it were me, I'd go to the local IRS office and request help from their reps to amend your tax return right there ... and they will do it for free. if you don't have an IRS office nearby, then pay a CPA or a tax-prep company to do it for you.
