If you mean that there is always the same base under the sequence base....say a G under all of the Cs then the likely reason is that all of the fluorescent spectra of the dye deoxy bases overlap to some extent and it is necessary to run a spectral matrix defining what contribution every base colour makes to the total peak height. This is read by the sequencer and used to clean up the electropherogram. If this file has not been maintained properly then some of the fluorescence will be interpreted as a base call.

If your sequencing is done "in house" then suggest that they run a new spectral matrix and if it is being done commercially then move supplier.