It depends what you mean.
On both sides, at the top & bottom, they're stems but if you mean brown spots on the inside for example if you left it in the fridge for about 1 day, don't worry about it, you can eat it. On the skin - if it's OK inside you can eat it but if its really brown or nearly black you should just throw it out or don't buy it - whichever.
:)
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They generally occur when refrigerated, they should be ripened at room temperature