A regular withdrawal for medical expenses is not the same as a withdrawal of excess (unallowed) contributions.
First, if you and your spouse were enrolled in HSA-eligible insurance for the entire year, your limit would be $7000 (unless over age 55 which would raise your limit.)
If you are being told you have excess, the most likely reason is you did not finish the interview and are jumping around from piece to piece. Turbotax assumes your contributions are non-allowed until you finish the health insurance interview and tell the program that you had qualifying HDHP insurance and were not covered by any other insurance for the whole year. I believe this can be accessed both from the 1099-SA interview and from the HSA interview on the deductions and credits page. Make sure you complete these sections.
If you did not have eligible contributions, and indeed had excess (not allowed) contributions, then to withdraw them is a special procedure, not a regular withdrawal. If you withdrew money through normal channels you must use it for medical expenses or it is subject to income tax and a penalty.
