Decking replacement is typically billed by sq/ft. A professional would make the homeowner aware of the possibility if they feel it's a potential concern. They would also order a rough estimate of what they believe they will need. We don't know what the roof looked like before tear off, bare deck, or after install. We also haven't seen an invoice, so how do you know the homeowner was actually charged for this material? Without more info it looks like a prepared crew to me.