Gauge Issues in Extended Gravity and f(R) Cosmology

We consider issues related to the conformal mapping between the Einstein and Jordan frames in f(R) cosmology. We consider the impact of the conformal transformation on the gauge of a perturbed system and show that unless the system is written in a restricted set of gauges the mapping could produce an inconsistent result in the target frame. Newtonian gauge lies within the restricted group but synchronous gauge does not. If this is not treated carefully it could in principle contaminate numerical calculations.