Recently, I wasted a bit (not really, a lot actually) time trying to fix that been missed before P&P and reflow. Basically, some parts/pins are not fully covered by a paste (let’s say an user error)… Well, this is not big issue on a board with big and bulky stuff, but a few dozes aka 0402 parts that spread around here and there on a panel, not easy to see straight away.
Wonder how are you doing an inspection (if any)?
As number of parts and their size are going opposite directions for upcoming projects, it will only hard to notice similar issues in the future.
I was thinking how to sort it out and come up with (stupid?) idea – compare PCB images before and after a stencil work
In short, 
 1) take picture of PCB as is
 2) apply a paste on (1) PCB
 3) take another picture
 4) we have an sample and expected result
 5) do same as (2) and (3) for another PCB
 6) compare (4) and (5) results
 7) is okay or not?
 
 Yes, programming is required (opencv or similar), but not a rocket science…