Graphene is a two-dimensional material with extremely favorable chemical sensor properties. Conventional nanolithography typically leaves a resist residue on the graphene surface, whose impact on the sensor characteristics has not yet been determined. Here we show that the contamination layer chemically dopes the graphene, enhances carrier scattering, and acts as an absorbent layer that concentrates analyte molecules at the graphene surface, thereby enhancing the sensor response. We demonstrate a cleaning process that verifiably removes the contamination on the device structure and allows the intrinsic chemical responses of the graphene monolayer to be measured. These intrinsic responses are surprisingly small, even upon exposure to strong analytes such as ammonia vapor.