Is not the clear sprue in its own bag? at least that's normal practice nowadays. I seem to have read that kit QC is by weighing the complete boxed kit, to quite close tolerances, rather than having someone look and say looks ok to me. Not casting any nasturtiums but there was an article in the hobby press a while back called 'the dark side of the spares box' or something like that. one of the common ones was someone opening a kit box in the store or warehouse and pocketing useful bits.
I'm sure this is a genuine case but there are many reasons for parts not found other than manufacturer quality.