I was stuck on 99% on this map for a while (even after walking on the Yomi platform) but found a little crevice that I missed, and could barely see on the map at all. It's on the east side, the Stonestump Wastelands, where the canyon ends. It was a faint little sliver; if you're having this problem, look there, north of the cactuar stone.
XBL/PSN/Steam Gamertag: HoogTheStampede Now Playing: FFXIII-2; FFXIII; Terraria; League of Legends
The reason you can't get to 100% on the first run is because you have to get up on top of a pillar to unlock 2 pixels of map space.
The only way to do this is to ride a Chocobo to the south end of the map, and glide over to that pillar.
In order to do that, you need to defeat the 3 Gigantuars in the area by activating their statues.
You then need to defeat the Goblins (Quest), and then defeat Ochu. Only then will you be able to ride Chocobos and get the last 1% of map completion.
It's not a glitch or a bug or anything; they did it on purpose, it's part of the progression path. Without getting 100%, that witholds 2 fragments from Academia, which, in turn, nets you 3 more Bestiary entries (Ochu, Immortal, Yomi), by directing you to those quests.
Playing FFXIII-2 and loving it! Proud member of team Toriyama!