Time Explorer

Here are a few tips for achieving 100% map completion in certain areas in Final Fantasy XIII-2 (FFXIII-2). I experienced difficulty in these areas and here are some parts of the map that are often overlooked.

General Tips for Map Completion in Final Fantasy XIII-2

• During your first visit to a new area, always try and explore as much of the map as possible to reduce downtime needed to return later as some parts of the map are only accessible during your first visit.
• If you missed some parts of the map that are only accessible during your first visit, just find the corresponding gate seal and close the gate to that area from the Historia Crux. This lets you replay that entire area as if it is your first visit (but you keep all records of opened treasure spheres and explored terrain).
• The dark blue areas on your map are unexplored areas. They become light blue when you travel over those areas. This makes it easy to track where you have already explored. Keep in mind that some areas have multiple layers so you need to check under the displayed map areas if any.
• The description of the map key items you acquire through the story have a "% explored" at the end. View your map key items to check which locales you have not fully explored. Alternatively, you can check a certain locale's exploration progress by opening the map via the square button.
• Some locales have multiple eras associated with them. To get a 100% map completion, you must fully explore ALL eras associated with that locale.
• Some parts of the map can only be accessed once you have the Anti-Gravity Jump fragment skill, chocobo access or key items obtained via sidequests.

New Bodhum

• The part that most people overlook is the NORA house. Walk over every inch of land in and around the NORA house. This includes the two sides of the patio that can be seen if you stand in front of the NORA house and look directly at it. Manually walk over the entire space of the patio; just going near them is not enough. The patio is not clearly noticeable as dark blue even if it is unexplored so the only way to be sure is to walk over it.

Academia

• There are a lot of corners and hidden alleys in Academia 400 AF and 4XX AF that need to be walked over manually. But this might come naturally when you are attempting the Captain Cryptic sidequest.
• On your first visit to Academia 500 AF, explore every part and make sure you step foot on every platform (especially the central platform that can be reached by jumping down from the two rotating platforms above it). If you miss this opportunity to get a 100% map completion on your first visit, you will no longer be able to reach most of the platforms once you have finished this part of the story. You will need to find the gate seal for Academia 500 AF, close the gate from the Historia Crux, proceed with the cutscenes until the boss fight with the two giraffe cie'th and regain access to block switches. DO NOT TOUCH THE BLOCK SWITCH. Instead, you can now reach the central platform again.

Augusta Tower

• Complete all three Paradox Agent sidequests to obtain Access Key 13 which allows you to reach floor 13 in some of the eras associated with this locale.
• You must fully explore every floor of every era to get a 100% map completion.
• Some eras only have access to certain floors so check every era.

Archlyte Steppe

• There is a raised stone formation south of the Nomad Camp near the edge of the map. You can reach the treasure spehere on it with Moogle Throw but you can't step foot on the stone formation without a chocobo. Anti-Gravity Jump will just miss it. 
• Touch all five cactuar waystones (four are red, one is gold) and defeat all three Gigantuar. Some waystones appear only in certain weather conditions. All waystones must be revealed with Moogle Hunt. After you have done so (if you touched the five waystones you should have the bottom five fragments on the Archlyte Steppe fragment list), talk to the person standing by the chocobo stables in the Nomad Camp to unlock chocobo access in this locale. Ride the chocobo to the cliff facing that stone formation, jump and glide to it. You should easily reach it if you're in the correct place.