To avoid bubbles, equilibrate media to the experimental temperature. Avoid temperature swings. If you work in a lab with strong air conditioning for instance, it is advisable to warm all equipment and reagents in an incubator to avoid spontaneous bubbles. Bubble formation may occur with use of the heater plate when there is a major difference between ambient temperature and experimental temperature. In this case, you might want to try insulating the plate, degassing buffers, or using a traditional incubator instead.
Degassing buffers using vacuum filters, vacuum extraction, boiling (autoclaving) or other methods may be useful in avoiding bubbles. Sometimes a bubble is lurking in the wells of interest or the serpentine from the priming process. Therefore before starting an experiment, always check around the well-microfluidic interface and in the serpentine for residual bubbles. Deal with them as above (plates).