The 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" can be debated as it is not always necessary, and some style guides may consider it optional.)
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We are passing through New Orleans, Louisiana right before we stop in Houston, Texas. (The use of a comma before the state name can be contested; some argue that it is unnecessary when the city and state are paired in this context.)
These two sentences have commas that may be considered non-essential or stylistically debatable based on different writing conventions.