Look at the monster design rules, and note the complete lack of "add proficiency bonus to stat bonus" to determine attack mods. Your assertion that these are "calculation errors" presupposes that monster stats are "calculated" in that way, when the rules pretty clearly state that this is not generally the case. NPCs and monsters are just balanced based on things like the charts in the DMG, they aren't constructed using shared rules the way they were in 3E.
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