Unfortunately we cannot open any attached files here. What is the unit for the y axis for the second plot? I believe for the first plot, the y axis is the power transmission? FDTD usually reminds you when the s-parameter is not passive, then there is an option to force passivity. It is also this option in INTC, and that's when you use the "force" passivity option, the power transmission will be forced to be lower than 1. If you see any warnings like the one you attached, you may want to force passivity in INTC.
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