There are three main causes for bubble generation on solvent based coatings: Air entrapment, Solvent flash-off and Too fast cure thick sections of coating.
In regard air entrapment, it is very difficult to apply coating to the topography of a circuit board without trapping air under some components. If you are accelerating the cure with heat these bubbles may not appear until the module is placed in the oven and the gas under the device expands due to heating.
The air, which remains under the component after cure, is not usually a problem: in some cases it is of benefit since it can act as a cushion during thermal cycling. A problem can arise when a portion of this air finds its way to the leads of a device and "pops" during cure leaving an exposed area. Also if the bubble is between pins or conductive paths this may lead to a weak point that may eventually allow corrosion, tin whiskers or dendritic growth.
There are several solutions: cold conformal coating (A CC with a lower temperature, 50-60 degrees F for example, will have a much longer batch time allowing the air to naturally escape and still have the coating flow to the space left by the busted bubble; A brief puff of air will often cause bubbles at the surface to pop, though care must be taken not to blow the coating off the area being coated. Even Rotation of the board or gentle agitation will assist bubbles to rise. The solution will be dependent on the module's design.
For bubbles generated by solvent flash-off by providing a period of time for the excess of solvent to flash off before taking the boards to a curing oven, the bubbles are minimized or eliminated. Also having again the coating a slightly lower temperature than the standard temperature (50-60 degrees F) will help with this issue.
Initial coating temperature as well as after-dispense cure temperature will affect both the solvent flash rate and the cure rate. Air movement around the board can similarly affect the flash rate and cure rate.
Finally for bubbles generated by an accelerated cure rate of the coating or extremely thick sections, mainly by trapping the cure byproduct some easy solutions can be applied. Provide the board some time before entering an oven will help.
Also heating the coating with a gentle curve, in opposite to as hot as it can get in a short time will minimize this kind of bubbles. If the wet thickness is above 15 mils you may need to cool the coating a little to reduce its skin over speed.
There are dozen of other probable causes however rarely seen, like gas absorption, coated that was pressurized for long time, organic contamination, etc. The suggestions above should most likely take care of the issue. Selecting also a low viscosity solvent borne silicone coating will help with this issue.