One should always wash their produce before use. If nothing else, because other people have handled the produce with their nasty bare hands, and who knows here those have been.
A small bruise, a healed over scar on the tomato, a slight shriveling on the pepper... Those things are death sentences to supermarket produce. they are literally thrown into a landfill. People think that a growth scar on the tomato means it has been mishandled. No, it means it was exposed to rain. Yes, RAIN. (Basically, when the tomato was ripening, it rained, and the tomato plant pushed lots of water into the fruit, and the skin could not contain the pressure, and it split. The fruit then healed over during the rest of the ripening process, leaving a brownish tough scar. It is a superficial blemish, and you should just cut that bit of skin off. No big whoop.) A slight bruise on the tomato can come from some slackjawed maroon being told that you should gently squeeze the tomato to determine ripeness, and not knowing what they are doing, and crushinating the poor thing. If you cannot tell the difference between a mishandled tomato, and a nearly rotten one, you should not be buying tomatoes.
For starters, ripe (and also nearly rotten) tomatoes have a distinct smell (respectively.) When shopping for produce, the appearance is inconsequential; you are going to cut the silly thing up, not turn it into a table decoration. Select for proper odor, texture, and indicators of proper ripeness. Most people do not know all the little things you should look for when selecting quality produce. Appearance is the least concerning. Bad texture from improperly ripened produce, bad (or worse still, ODORLESS!!) smelling produce, and produce with active decay are what you should avoid, not uniformity of color, shiny skin, uniform shape/size, etc.