After the resistance update my discovered locations tally is 296, but my completed locations tally is 306. 
Must happened because of the 10 bottle collectables, because there was something new to complete.
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What you do “wrong” is you play multiplayer and somehow that messes-up the real numbers. And maybe playing with different characters also effect the tallies, not sure about that though.
It looks like the game just add to the numbers, instead of checking if the player already been there , or did that mission, etc.
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Snipergirl, I have kept strictly to solo play, and I had to decline some of my Steam-friends requests who wanted to play together. So I am hoping my number counts are the real deal. 
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I have 449 locations discovered but that’s including the dlc island
I guess you discovered locations in multiplayer (as client), too.
This counter sadly counts everything, not just from your own game.
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