In the screenshot you provided, we can clearly see that the Stones are still covered in a crystalline material. This is most obvious with the purple Power Stone, on which we can see clear black-ish rugosities covering the Stone. The yellow Mind Stone in the upper-left corner also clearly looks encased within that material.
I would wager it was a primitive form of the Stones, from before they were found and refined (or left to their own devices). In your picture, we can make out the Stones' spherical shape from within the crystalline mineral, which would infer everything else is dust and debris caught through drifting in space, or something similar.
Once the Stones are recovered, they are always used through a customized container, in which they are purely ovoid. This can be easily seen when they are fit into Thanos' glove :
But remember the first movies. The Space Stone came within the Tesseract, into which it was contained through unknown means. Although the Tesseract is famously cubic, the blue Stone is ovoid (as seen in the previous picture, right under the middle finger). Likewise for the Power Stone : although it was contained in a bigger metal sphere, its size and shape is coherent with the other Stones.
We never properly saw the Soul Stone's being contained, as it was located somewhere in a pit on Vormir. That said, when Thanos held the stone within his hand, it clearly was round :
Likewise, the Mind Stone was encased within a blue crystal, powering Loki's scepter. When the Mind Stone was integrated within Vision's forehead, everyone could see it was indeed round.
The Time Stone was recovered through unknown means by the sorcerers of Kamar-Taj and transferred into the Eye of Agamotto... in which, once again, the stone is round :
Ultimately, once cleaned and prepared for use or containment, the Stones are naturally ovoid shapes. The only exception is the Reality Stone, or the Ether, which frequently manifests as a liquid-like cloud of energy, able to condensate back into a Stone. There is no current explanation for this phenomenon in-universe, other than its peculiar powers may grant the Reality Stone slightly different properties. After all, if the Soul Stone can manifest wisdom, why can't the Ether change its own reality ? (But that's only a guess)