I've written a few times about potential and actual problems with different PCB finishes. Sometimes, the results are tragic and sometimes, just annoying. I'm not sure where this one falls on the continuum between the two extremes, or maybe even outside. I suppose it depends on who's paying the bill and how close these need to be to a final production product.
The surface on the pads had been exposed to the elements a little too long such that, even with good flux, the solder balled up instead of adhering as it was supposed to.
PCB finishes are more robust then they were even a few years ago, (although, a few years before that when we were mostly using leaded HASL, things weren't so bad) but still, your raw boards should be treated more like food then like shoes. Avoid fingerprints and other contaminants. Try to use them promptly. Store them properly. If your air quality is poor, be even more cautious in your handling and storage.
Let not the sands of time get in your lunch