Its because not ALL Mega Stones are in one version. If you've seen Charizardite X/Y or Mewtwonite X/Y, they belong to their respective Versions. Also, certain Mega Stones are in separate Versions. All X/Y Stones as well as the rest listed below are obtainable in both versions. The other two lists are for X and Y Stones only found in their versions.
- Abomasite - Frost Cavern(After beating Team Flare that tries to catch it)
- Absolite - Kiloude City(After beating Serena/Calem for the first time)
- Aerodactylite - Ambrette Town(After finding the Scientist in Glittering Cave)
- Alakazite - Reflection Cave(Hidden Entrance. Look through a Mirror in a dead end)
- Ampharosite - Azure Bay(From the old man in the island in front of the Sea Spirit's Den)
- Banettite - Chamber of Emptiness(Find the sparkly spot :3)
- Blastoisinite - Professor Sycamore's Lab(Select Squirtle as secondary Starter/ Stone Emporium)
- Blazikenite - Event/Omega Ruby and Alpha Sapphire(Event Torchic from Launch Day to Jan. 15th this year)
- Garchompite - Victory Road(Northern Exterior Section to the left of the Ruined Tower. Requires the move Rock Smash to break the stone wall)
- Gardevoirite - Trade with Diantha(Trade ANY Pokémon with Diantha in Café Soleil in Lumiose City)
- Gengarite - Laverre City Hex Maniac( Look around to find a Hex Maniac. To get it, you must have Ghastly, Haunter or Gengar seen in the Pokedex)
- Gyaradosite - Couriway Town(Hidden in the area of tiny waterfalls, behind the Water Bottle Dealer)
- Kangaskhanite - Glittering Cave(Find the Sparkly Spot again :3)
- Lucarionite - Tower of Mastery(Accept the offer from Korrina)
- Mawilite - Shabboneau Castle(Find the Sparkly Spot yet again :3)
- Medichamite - Laverre City(Find the Sparkly Spot... in front of the well! :3)
- Scizorite - Frost Cave(BEHIND the Abomasnow. The same one you got the Abomasite from)
- Venusaurite - Professor Sycamore's Lab(Select Bulbasaur as Secondary Starter/Stone Emporium)
Pokémon X Stones
- Charizardite X - Professor Sycamore's Lab(Select Charmander as second starter in X/Stone Emporium in X)
- Manectite - Route 16(Find the Sparkly Spot by the bikers going in a circle around a hill in X :3)
- Mewtwonite X - Unknown Dungeon(After catching Mewtwo in X)
- Pinsirite - Santalune Forest(Find the Sparkly Spot in X :3)
- Tyranitarite - Cyllage Gym(Find the Sparkly Spot in X again :3)
Pokémon Y Stones
- Charizardite Y - Professor Sycamore's Lab(Select Charmander as second Starter in Y/Stone Emporium in Y)
- Aggronite - Cyllage Gym(Same as Tyranitarite but in Y)
- Heracronite - Santalune Forest(Same as Pinsirite but in Y)
- Houndoominite - Route 16(Same as Manectite but in Y)
- Mewtwonite Y - Unknown Dungeon(Same as Mewtwonite X but in Y)
I worked kind of hard on these lists. The source is Bulbapedia.
Also, the "Find the Sparkly Spots" Refers to use the upgraded Mega Ring. Upgrade it by first defeating Serena in Kiloude City, then go to Anistar City to the Sundial and talk to Sycamore to upgrade the ring.
Hope I REALLY Helped!
Edit: By the way, Post Game is basically the Aftermath of an RPG. Many RPGs have this besides Zelda. To get to a Post Game, you'll need to defeat the Champion for the first time. There are a bit of spoilers in the very end, so I'll leave them for you to check out.