It sounds like what you're doing is pressing a sticker on the inside of the base of the bottlecap, then filling the bottlecap with clear embossing powder and baking to melt it, then using the finished bottlecap as what? if not as frig magnets...just for the girls to swap?
Anyway, you could be having several problems with the embossing powder and/or stickers... at least these:
...too much heat for the embossing powder (or oven not preheated, or has hot spots), which could cause it to bubble or darken
...air trapped around the edges of the stickers (or moisture) could be turning into bubbles
...material stickers are made from could be warping in that much heat, or stickers can warp since one side will shrink a bit with heat but the other side won't
...sticker colorants could be dissolving in embossing powder and bleeding and/or causing moisture/steam/bubbling
Baking the embossing powder and all the bottlecaps at the same time does save time, but you could let the girls melt the powder with embossing guns depending on how many girls you have. Each bottlecap would take a short time and the process on each bottlecap could then be carefully watched and stopped if anything bad starts to happen (make sure the girls know to gently
wave the gun around while heating so no area will overheat).
You could also use other clear coatings to pour into the caps, or brush on in a couple of coats if you have time.
Epoxy resin is the most common thick coating in bottlecaps, but if you don't want the bother of using resin or its expense and setting time, you could use one of these things:
...2-part epoxy
glue ("Devcon's 20 Ton," is one of the clearest, though not cheap)...the 2 parts would be extruded in small amounts on a tile or something and mixed together, then picked up with a toothpick/etc and dropped into the bottlecap...sets up fairly quickly compared to regular epoxy resins
...clear polyurethane (cheap) ...or clear acrylic fingernail polish (more expensive)
...**cyanoacrylate floor polish --Mop 'N Glo, or Pledge with "Future" Shine -- (cheap)
...acrylic mediums--probably gloss acrylic medium for this-- (medium-cost)
...dimensional white glues like Diamond Glaze, Crystal Lacquer, etc (expensive)
...plain permanent white glues (PVA, craft glue) perhaps thinned down with water, or ModPodge and other decoupage mediums ...may not be as totally clear as you'd like if in one thick pour though (pretty cheap)
All of the water-based materials (not the resins or epoxy glue) "dry," but will take different amounts of time. Some will set up fairly quickly and could be taken home to finish drying if at least a little care is taken.
The drying of some can be speeded up a bit in a low-heat oven (say less than 225-250 F or less), or even in front of a fan.
The water-based ones can also be colored with a bit of acrylic paint.
You might want to check out some of the info I have on making bottlecaps like this on this page of my site, and how the images (or stickers, etc) are prepared and adhered for best results:
http://glassattic.com/polymer/other_materials.htm (click on
In Permanent Cells, under Epoxy>Casting then scroll down to the bottlecaps area)
And this page has more on the various kinds of clear "finishes" that are often used in arts and crafts, including the ones above:
http://glassattic.com/polymer/finishes.htm** the floor polishes are fairly thin in consistency... they can be used as is, or will thicken up if left out overnight or in an open container for a couple of days
) advertising by donating a challenge prize! 
