To prevent the condition you're observing you should consider silver or
ceramic fill...with solder mask fill it's almost impossible to properly fill
them to a degree they will not entrap contaminates such as solder or flux.

When specifying "solder mask plug" on purchase documents you can expect to
see the all the copper in the via covered with mask but also see those pits
or voids in the mask caused by shrinkage during cure. This is typical, and
by all definitions it is indeed "plugged".

So if the goal is to have vias that will not entrap anything, then having
them filled with conductive or non-conductive materials such as silver or
ceramic, and then capped with copper and mask over the cap...

Franklin

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