Not enough info to provide detailed examples, but the incorporation of surfactant may help. How about doing a better job of degassing (i.e. try in-line degassing or continuous sparging with pure helium). Another example: Select a better surface material (polymer or coating) which is not attracted to the liquids.
This always happened when I worked with the engineering researchers in the past. Although the suggestions from both Erich and Bill can be great help to get rid of air bubbles within the small chamber like microfluidc devices, degassing and use of surfactant may give different effects on the culture.
The first thing is the CLEAN device without any fault for fluidal stream. Then removing remnant toxic chemicals by extensive washing with sterile ddH2O several times, follow by complete and gentle drying.
Secondly, it's very simple care not to get any air bubbles within the chamber by WARMING 1) medium in a 13 ml culture tube medium, 2) a syringe fitted with needle and 3) tubing system in CO2 incubator overnight. Usually you are generating air bubbles from medium and device system kept at cold or room temp. The microdevice appears to be OK immediately after you prepare for cell culture under a microscope at room temp. However, after the medium and device system get warm in the CO2 incubator, the air bubbles generated from the cold medium could not escape, and are trapped. So EQUILBRATE EVERYTHING WELL BEFORE (OVERNIGHT) WHITIN THE INCUBATOR in the aspect of TEMPERATURE!!!
Finally, when you observe or take image records of the cells in the chamber, WARM UP the atmosphere and cold microscope stage by PUTTING A LIGHT ON on the stage well in advance to avoid cold and warming cycle. You never generate any bubbles within the chamber.
It is a good idea to maintain the microscope and culture room at just above 30C by air conditioning of heating system for microfluidic cell culture works.