yes the cause is operator error. However, the solution that won't work is to train them, admonish them or discipline them. The underlying causal mechanism of 'operator error' is that the system allows them to make the error or mistake and so they will. It is fundamental human nature. (and why we invented spell checker - I can spell perfectly well, I just can't type the letters in the order they were intended to be typed

)
So mistake proofing is the appropriate corrective action if you must reduce the defect rate. Most error proofing schemes are relatively cheap if you put some thought into them.
A place ot start in this situation is to determine why the operator didn't follow the procedure - is it too complicated? did he deliberately choose to not follow it? if so why? did he really not understand the consequence of short shots beign shipped to the customer or did he think his supervisor was more interested in quantity than in quality? Perhaps he thought that there weren't that many short shots and he was saving the company money? (there is a slight difference between unintended errors and intentional mistakes)
these questions can provide insight into what steps will work to prevent the occurence in the future...
some simple tools that help ensure that the start up parts are culled and scrapped: if there is a set number of shots to successful startup, have a 'bin' that either counts (thin egg carton) or weighs (depending on size) the startup parts and this bin must be filled and accounted for before parts can be moved into the 'good' bins or stream. perhaps a simple countere can be used to manage a diverter switching from the startup scrap stream to the good stream once a specific count has been reached?
But the best approach that I've found is to ASK the employees how they think the process can be improved....