An innovative methodology for visualizing and identifying some mechanisms by which complex structures such as air-in-oil-in-water (A/O/W) and water-in-oil-in-water (W/O/W) may be formed inside mixing tanks dispersing various phases is described. In the case of A/O/W inclusions, isolated inclusion events could be observed by the first time with an experimental setup designed to produce sudden turbulence in a small confined space simulating a three-phase fermentation system. It was observed that high-energy direct-collisions of the bodies are not required for inclusions to occur; rather, a gentle contact between the phases was needed. Then, by maintaining an oil drop in a fixed position while it was impacted by single air bubbles, it was feasible to calculate the percentage of air-bubble inclusions into oil drops for different compositions of the continuous phase. By adding biomass as a solid phase, the inclusion occurrence reached 61%; likely this was caused by a mechanical effect of the added biomass (making the interface breakable or unstable) with a minor contribution by the decreased surface tension. In the case of W/O/W, a basic mechanism by which the inclusion of water droplets in oil drops may occur is described. This was derived from the analysis of the hydrodynamic process of the formation of a water drop inside a volume of oil where the differential pressures occurring along the water-oil interface were mapped. This is the first time that factors influencing water and air inclusions in oil drops are identified, and possible mechanisms behind their occurrence are proposed, based on visual evidence.