I haven't been able to discern a pattern, but sometimes when I retrieve my bloodstain after dying, it holds roughly 20% fewer runes than I dropped when I died. I've seen threads elsewhere on the internet that say nearby enemies will pick them up - and I have come across mobs (both hostile enemies and non-hostile creatures) with glowing gold eyes that drop far more runes than their non-glowing counterparts. However, there doesn't seem to be any relationship between these mobs and my mysteriously light bloodstains: I've come across them seemingly randomly in the wild (including two enemies in a tomb I'd never visited before), and I've thoroughly examined the surrounding environments when I've noticed my bloodstain is smaller than expected and come up with nothing - so if there is a relationship between the two, it's not an obvious (or geographic) one.
I was noticing this too, particularly in Stormveil Castle when I was
fighting dying to Godrick. Each time I collected the lost runes, I was noticing a decrease of what seemed to be about a third of what I initially had. It turns out this loss is due to an NPC you meet at the very beginning, when you first ventured into Stormveil Castle, when you met Gatekeeper Gostoc.
Gatekeeper Gostoc is the NPC you meet just next to the main gate to Stormveil Castle. He'll explain to you that you shouldn't take the main gate as it's too dangerous, and you should instead take the side passage next to him. Per the wiki:
Gostoc at first may seem to want to help the player, although in a suspicious manner. This is however just a facade. He will actually steal 30% of your runes every time you die in the castle, even if you enter it through the main gate.
So, while Gostoc lives, each time you die within the castle, you will permanently lose 30% of the souls you originally had. Gostoc's influence also appears to extend to a difficult-to-measure area around the castle, as his influence appears to be a bit larger than just Stormveil Castle. This influence appears to extend to somewhere between Stormhill Shack and Warmaster's Shack.
Once I learned that this was occurring due to him, I went and killed him, and I noticed that since then I wasn't losing 30% of my runes upon death.
You can find Gostoc stalking you in certain locations throughout the castle, which I suppose from a lore perspective explains how he's able to steal your runes each time you die: He's always watching. According to the wiki, he's also the reason you're locked in the room that contains the Rusty Key, as when the cinematic plays you can hear Gostoc cackle as the door slams shut.
Killing him will also give you Gostoc's Bell Bearing.
It is possible that there are other NPCs that will also siphon runes similar to how Gostoc does in other places throughout the game, but I haven't noticed this effect elsewhere yet.