Retirement Plan Contribution confusion?

My wife gets a W2 from employer and a small 1099-Misc income from others. She contributes max to her employer 401k. Turbo Tax maximizes SEP contribution on her 1099 income and she contributes that. This year it is confusing - it is showing zero under SEP, but total qualified contribution that exceeds her 401k contribution. Does that mean she can contribute zero to SEP or calculate difference between total less what she put into 401k to put into SEP? Surprised that Turbo Tax is not pulling her 401k contribution from the W2 and showing zero instead? PS: Does employer match count also? That is reported nowhere.