Flow Cytometry is a measurement technique used in Quality Control and in-process measurements of biomanufactured Cell and Gene Therapy products. However, it contains a number of sources of measurement variation at; sample preparation, instrument setup, analysis, and post-analytical data analysis stages. The latter sees variation introduced from operator subjectivity, which is investigated here to understand what effects the interpretation of diagrammatical protocols have on inter-operator analysis. 36 operators from different sites were given a series of histograms to analyse, gating a shifting peak. This was repeated with diagrammatical protocols to apply gates which reduced inter-operator variation by up to 92%. Various control limits include and exclude different results and when adjusted with a log transform differences in outlier discrimination have been found. This research supports the use of Flow Cytometry diagrammatical protocols to reduce the contribution of inter-operator variation and measurement uncertainty associated within Cell and Gene Therapy manufacturing scenarios.