We investigate the transport properties of three-terminal carbon-based nanojunctions within the scattering matrix approach. The stability of such junctions is subordinated to the presence of nonhexagonal arrangements in the molecular network. Such "defective" arrangements do influence the resulting quantum transport observables, as a consequence of the possibility of acting as pinning centers of the corresponding wave function. By investigating a fairly wide class of junctions we have found regular mutual dependences between such localized states at the carbon network and a striking behavior of the conductance. In particular, we have shown that Fano resonances emerge as a natural result of the interference between defective states and the extended continuum background. As a consequence, the currents through the junctions hitting these resonant states might experience variations on a relevant scale with current modulations of up to 75%.