I had to actually re-watch the episode... and I must say: Very well spotted! There is indeed a stone resembling one of the "petrified" Element of Harmony in Spike stash.
You can see it for a brief second soon after Spike discovers that his voice has changed.
comparing it with Season 1 episode 2:
that is the same shape/asset, reused in this episode.
That said, I don't think it should be given any importance: it is probably just an error the animating staff made. Every scene that show the stash before shows a strange red sphere (which someone may recognize as one of the bowling balls from the S02E06 - The Cutie Pox episode) in its place, so sake of simplicity suggests that the assets just got switched in that single clip (I would even go as far as saying that probably they have a library or round stones and inadvertently used one in place of the other). Probably there is nothing more to be seen into that.
or at least, until you notice the colors of that red/orange sphere and then get on head-canon tour about the sphere begin a reference to Sunset Shimmer and to the alleged 7th element.... :P
.... which is obviously totally unsupported by the show canon so far.
It is also worth noticing that while we don't really know what those stones actually where in Season 1 (where those the actual old Elements Celestia used, now turned to stone? does that mean that the "current" Elements are a new set - at least at a physical level?) it isn't actually possible that the stone in the stash is one of the same stones we saw in season 1. Nightmare Luna smashes the five original stones, and the sixth one (bearing a different symbol, Twilight cutie mark to be precise) only appear when the true nature of the Elements is revealed. At the same time, the stone fragments turns to the Element necklaces we can see in the future episodes. No stone seem to have survived the morph.
Thanks to Ellesedil for pointing me to notice that.