When you handle the plates, try not to apply pressure to the coverslip glass on the bottom – it can be cracked easily in this way.
When priming channels of interest, it is important to inspect channels after priming to make sure that the entire path has been filled with liquid. If you see bubbles upon initial priming, you may remove them by ramping up shear to higher levels. If this doesn’t work, it may help to push fluid all the way out of the channels and reprime. Repriming with 50% isopropanol might be of use as it has lower surface tension and fills in the microfluidic path better than water (follow with a water wash). Finally, if this doesn’t work, prime channels with water, fill the wells with equal amounts of fluid and leave overnight. The gas may dissolve.