Nowadays, in modern management and control applications, line parameters need to be known more accurately than in the past to achieve a reliable operation of the distribution grids. Phasor Measurement Units (PMUs) may improve line parameters estimation processes, but the accuracy of the result is affected by all the elements of the PMU-based measurement chain, in particular by the instrument transformers. Current transformers (CTs) are nonlinear and therefore their behavior is not easily described: their models cannot be straightforwardly included in estimation problem. In this regard, the paper refines modeling and compensation of CT systematic errors in line parameters estimation processes, based on different methods to describe the transformer behavior under various operating conditions. As main result, the systematic errors of CTs are remarkably identified and mitigated. Moreover, estimation of shunt susceptance values is significantly improved.