Why are stems common in packaged raisins but uncommon in breakfast cereals?
I've noticed a difference between raisin brands in the past. Given my habit of alternating weekly shops between the close/cheap supermarket and the well-stocked one I'd choose to buy them at the better shop, though I've had worse than even that cheaper shop.
From the better shop I find less than one stem in a generous handful of raisins (on my otherwise plain weekday Weetabix), but in the worst ones I've tried I've found a few every day.  This all indicates that there's a possibility for variation from some point in the production process.
Given that variation, so long the worst ones aren't added to breakfast cereals, and given the dilution by other ingredients, I'd expect to find very few.
In addition, there's no guarantee you'll find every single one.  On weetabix or porridge I've been known to spot a stem only to lose it when it sinks, but then not to find it when eating.  In something like granola with its range of textures and harder components I would be more likely to miss an occasional stem.