The crash was caused by a failure of the Mercedes driver's Brembo-supplied brake disc, so Mercedes opted to switch the Briton to Carbone Industrie brakes ahead of the grand prix.
Mercedes successfully argued that it should avoid penalty for breaching parc ferme rules because of a clause allowing changes if the new parts are "similar in mass, inertia and function".
Christian Horner revealed that he "absolutely" disagrees, particularly as both of the Red Bull cars were fitted with Brembo brakes throughout the race weekend.
"If you change it like-for-like that is one thing," he said.
"But if you change it for something made by a different manufacturer that has a different characteristic, and as described by the driver himself as something different, it is an interesting precedent."
Horner ultimately decided not to protest, but he is now calling for an FIA "clarification".
"We obviously now need clarification," he said, "because if you can do that, then what else can you change?"
Ferrari's Marco Mattiacci also admitted discussions took place about a potential protest.
"We decided not to move forward on this because I don't think we wanted to get into it," he said.