We had previously reported appropriate performances of automated AQUIOS CL cytometer (Beckman Coulter) for regulatory approval of absolute T cell enumeration. However, after 4 years of routine use, we still observed recurrent histogram anomalies that may affect both absolute values and T cell subset percentages results. The objective of the current study was thus to perform a cross‐sectional evaluation of these graphical anomalies within a university hospital context, to assess their influence on results and ultimately to propose a standardized decision tree to circumvent graphical disturbances at the time of results validation. Eight hundred and sixty‐two blood samples were prospectively analyzed on AQUIOS CL. Results were compared to (i) lymphocyte values from complete blood count; (ii) results from manual staining and analysis on Navios cytometer (Beckman Coulter); (iii) results after washing step and reacquisition on AQUIOS CL. Nearly 75% analyses did not show any graphical anomaly. 20% had single anomaly on “Lymphs (45)” or “Lymphs EV” regions influencing T cells percentages and requiring manual re‐gating of “CD3− capture” region. 5% showed concomitant “Lymphs EV” and “Lymphs (45)” anomalies influencing both T cell percentages and absolute counting and requiring additional staining and analysis on Navios. Finally, <1% presented with anomaly on “CD4/CD8” histogram or “CD3+ All” region, influencing both T cell percentages and absolute counting. Around 25% AQUIOS CL results were flawed due to gating anomalies. In <5% cases, additional back‐up procedures should be undertaken to ensure results validity. A simple decision‐tree may help in guiding validation process.