Once you store them as Sounds, then perhaps multiple instances of the same sample isn't an issue anymore. Effectively, as I understand it, once you're working with a Sound, it's its own unique entity with its own tag, ID or whatever, and can no longer be confused with anything else.
I think what happened to me, was that the Digitakt called on the same instance on the drive - the same source - and just didn't get why there were multiple calls for this from the same place. I know, it sounds far fetched, having no insight in the Digitakt's core structure, but it would make sense - essentially the same as trying to store two files with identical names in the same folder. Though you can't, in any other case, and if you try, you're either stopped or suggested to rename it. If not, this kind of chaos might be the result.