This study identifies and addresses some major pitfalls that are involved in the visualization and quantification of the gas-liquid distributions and their profiles in a bubble column with internals using the gamma-ray computed tomography (CT) technique. Some of these pitfalls encountered in the scanning of bubble columns with internals are using an improper reference scan, and applying the same experimental scanning procedure and mathematical relationships for estimating the gas holdup in the column without internals to the column with internals. The experimental results revealed that the selection of the inappropriate reference scan for CT experiments would significantly affect the reconstructed linear attenuation coefficient values and consequently the gas holdup results. Additionally, the reconstructed linear attenuation values showed good agreement with theoretical values when considering air as reference scans. However, disagreement is observed when using the empty column with internals as a reference scan. Moreover, it was found that using the proper reference scan eliminated the errors not only for the reconstructed linear attenuation coefficients but also for the gas holdup values near the wall region. Furthermore, the CT technique was capable of capturing the small thickness (5mm) of the wall for phantom and bubble columns as well as the internals when the air was used as the reference scan. Finally, a new methodology has been implemented to exclude the internals from the cross-sectional images, and the azimuthally averaged gas holdup profiles to provide accurate and reliable results for comparison and validation purposes for the bubble column with internals.