The two sentences that use a comma in a way that is considered contested usage are:
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Stephen did not understand the question, and so Gina tried to explain it to him more clearly. - The use of the comma before "and so" is contested because some style guides suggest that a comma is only necessary when "and so" introduces a new independent clause.
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We are passing through New Orleans, Louisiana right before we stop in Houston, Texas. - The comma usage before "Louisiana" is technically correct; however, there can be discussions regarding the use of a comma before "right before" as well.
While both sentences use commas correctly according to some conventions, their usage can be questioned or debated in some contexts, making them potentially contested.