Phase-imaging ion-cyclotron-resonance technique has been implemented at the Penning-trap mass spectrometer JYFLTRAP and is routinely employed for mass measurements of stable and short-lived nuclides produced at IGISOL facility. Systematic uncertainties that impose limitations on the accuracy of measurements are discussed. It was found out that the phase evolution of the radial motion of ions in a Penning trap during the application of radio-frequency fields leads to a systematic cyclotron frequency shift when more than one ion species is present in the trap during the cyclotron frequency measurement. An analytic expression was derived to correctly account for the shift. Cross-reference mass measurements with carbon-cluster ions have been performed providing the mass-dependent and residual uncertainties.