First, "pendant" size bottles would be too big for most miniatures (what you're calling "charms"). You could use slightly larger bottles though, or just use teeeeny miniatures.
As for where to buy miniatures though, you can often find them around Christmas or other holiday times as mini-tree ornaments, or as other embellishments and jewelry, etc, or at hobby stores for model railroads/etc, or as kids "buttons," or in craft stores with the jewelry components or with the scrapbooking supplies.
You can make the miniatures yourself though, and you can make the settings/etc too.
In the case of this company, a lot of their miniatures are mini trees, flat figures (paper, plastic or cardboard, etc, probably die-cut in their case), dirt/grass/water made from stuff like clays/model railroad grass or dirt and bits of mini trees or tree-making stuff and also resin. Some of the flat figures, etc, might also be purchasable as special shapes of plastic "sequins," or they could be created from shrink plastic.
https://www.google.com/images?q=tiny+world+in+a+bottle
You *can* make miniatures and mini-dioramas like this from any material you want though (especially since they'll be protected by being surrounded by glass). Mini trees/bushes/etc can also be made by cutting off a small portion of some kind of artificial plants, flowers, etc, from craft stores:
Check out some of these pages at my site for more on making minatures and dioramas (with polymer clay, or you could use air-dry clays or other materials), plus some other answers of mine and more sites:
http://glassattic.com/polymer/miniatures.htm
http://glassattic.com/polymer/houses_structures_gingerbread.htm
http://glassattic.com/polymer/kids_beginners.htm (click on "Scenes & Dioramas," 3/4 of the way down list)
http://glassattic.com/polymer/outdoor_snowglobes_fountains.htm (click on Basics, then check out some of the "items")
https://answersrip.com/question/index?qid=20110603192436AAGG4s1
And you might be interested in one of the little bottles I turned into a mini scene with tree, cabin, and snow as a "snowglobe":
(THIS LINK plus one other moved to below)