I have never heard the phrase at all, but this is the definition online:
"A negative externality is a cost that is suffered by a third party as a result of an economic transaction. In a transaction, the producer and consumer are the first and second parties, and third parties include any individual, organisation, property owner, or resource that is indirectly affected."
It seems to have arisen in the economic sphere - I could not find any references to it in relation to RTAs, except as regards that economic spin-offs.