I find the use of "run" in that context rather unnatural. I would expect to hear it in something like this:
Jane: What size shoes do you wear?
Helen: Normally a size 5. However, if I buy shoes in Braxman Shoes, I get a 4 because the shoes in there run large.
Note that in BrE, it's more common to say "the shoes come up large" in the shoe context.
For apples, I would use "The apples are large" or "The apples grow large".
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