It sounds like you are entering the contribution in that area of the program for Traditional IRAs rather than in the area for a SEP, so it is adding a penalty for excess contribution. Switch to Forms view and look to see where the contribution is going, look for additional taxes and schedules to give you some clues, and make sure you are seeing the SEP in the proper place on the tax form. (A SEP contribution will be on Schedule 1 Line 15, a traditional IRA on Line 19.)
The SEP-IRA contribution doesn't go in the section for Traditional IRAs. It goes in the section for "Self-employed retirement plans". You should be able to search the term "SEP IRA" in the search box to find a link to it. If that doesn't work, it is located in the section for Business Income & Expenses under Less Common Business Situations, then Self-employed Retirement.
