I've never used rubbing compound, so I don't know an answer.
Though, I wonder why it was used on a fairly new vehicle.
From what I remember, rubbing compound is a fine liquid "sand paper" that removes the upper surface of paint and is used to remove oxidation and the like. As such, it removes paint. A "repair" would involve smoothing it out. The best way depends on the depth of the surface and the amount of surface material/paint/clearcoat removed by the compound. a good waxing or whatever the recommended finishing for the rubbing compound should remove minor scratches. If greater, have a detailer (more experience, tools, and supplies) look at it and tell him/her exactly what you need.
Again, I am using reasonable speculation and educated guessing. A detailing expert would be better. I have "issues" washing my car(s) more than once a month, averaging once every 1,000-2,000 miles . . .