Is there some reason that crystal footprints such as Crystals:Crystal_SMD_HC49-SD have pads that appear in the solder mask but not in the paste stencil layer?
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The creator probably forgot or disabled the paste layer for those?
If I were you I’d report this on github and if possible provide ‘repaired’ footprints in a pull request.
Don’t encourage people to do just that 
@Tom_Cook
Pleas fix it. I bet they have other library convention (KLC) violations aswell!
If you are willing to contribute have a look at the new KLC and maybe also look at the FAQ both created mainly by @SchrodingersGat.
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