Sounds like they were cut a tad big or pushed in a little too far

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As you describe it I'm sure it's just a very minor imperfection that only YOU notice. Tell your wife that I agree with her.....and to 'smoosh' it down a little. You might use a couple paint stirrers or something other than your fingers to do the 'smooshing'. Since it was the wifes idea you might let her do the 'smoosh'

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FWIW these little blemishes always seem worse than they are....you won't notice it by the end of the week! You'd be surprised what finish (sanding) primer can cover.