Does the fruit label get put on a bad spot, or does the bad spot develop as a result of the label?
A few years ago I had the rare chance to take a look behind the scenes of the largest manufacturer of fruit sorting, labeling and packaging equipment in the Pacific Northwest and it was impressive to see how much effort and planning goes into designing everything in a way that damage to fruit is avoided at all costs. We talked about how the business evolved and what the biggest challenges are. 

And yes, the stickers are a crucial part. Developing a glue that is food-safe, will stick well and come off without damaging the fruit is a challenge and different manufacturers have solved it more or less well. If you observe carefully, you will notice that the stickers will behave differently.

There are two main ways how stickers can lead to damage:


Too much local pressure when applying the stickers and 
A glue that is too sticky and tears the fruit when the sticker is pulled off.


The former will result in a soft spot or other blemish, the latter is visibly fresh. Soft-skinned fruit like peaches are much more prone to damage and a real challenge compared to e.g. apples. The damage is not unavoidable, a lot depends on the settings of the equipment and a good operating personnel.

But I can assure you that no fruit packaging plant will “cover up” blemishes with a sticker - simply because they label way too many pieces per hour. Blemished fruit will be sorted out before packaging, damaged fruit in packs will typically mean the whole package is rejected by wholesalers - because they won’t travel and store well. 



Knowing all this, one of my pet peeves is supermarket workers that think refilling displays is best done by upending boxes of apples, but that’s not part of your question.