This is actually a known issue or something, there’s a thread where they talk about this stuff and that trickles back to elektron. It’s not MP3’s specifically, it has to do with something else, probably the way it attempts to negotiate a zero crossing slice on a stereo file which will obviously not often have aligned zero crossings between L and R waveforms. This is just my guess at what’s going on though, some people believe it’s a “bug” but the behavior is pretty consistent.
I think it does this with any sampling of fixed length. Like you could import a sample with a bunch of silence before and after and manually trim it down to size but that sounds like a headache. Digitakt 1 which is mono doesn’t do this, so one would assume it has to do with the stereo capabilities.
There are several existing reports about this, and someone did a pretty good job of illustrating the actual issue using the waveforms themselves. I’ll find you a link so that you can add your complaints to the proper sections of the forum, maybe that way they’ll find a way to do something about this.