I had a similar problem with a return. Box 12 of the W-2 had code W and the amount entered. The problem I had delt with the way the employer entered wages on the W-2. On the state wages the employer added the amount of HSA contributions to the state wages showing a higher amount of taxable wages to the state. Turbo Tax picked this difference up as excess contributions and created a penalty tax. When I changed the state wages on the W-2 to match the Federal wages it corrected the error. I don't know if this applies to all states, but it made a difference on Arkansas. This corrected the Federal return and treated the HSA contributions correctly.
