As of 1.00.7, a few of the Upgrades got swapped around to different levels. Lvl 3 beam no longer appears in Vulpine, it appears in Raccoon. Air jump is in Snapper, and Rapid Shot is in Vulpine. The capsule is probably not there because you have the buster upgrade already, even though you got it from its original location in an earlier save. I'd start a new save file. Or, just go back to Snapper stage and you should find the capsule pop up there again. Test it out, I'm curious.
So I went to Snapper's stage and found the capsule there, but when I got inside the animation didn't activate and I couldn't get the upgrade. I thought of going back to the 1.007 version and going to racoon's stage to get the upgrade there but the same thing happened. It seems I can't get the upgrade anymore and I have to start a new file