I found a way to reproduce the issue.
Here is a Video where I first bounce out another audio before applying free warp, it just looks and sounds like the original.
If I now stretch the waveform at the end, the error message appears, and the audio is messed up, as you can see in the render/bounce as well.
EDIT: here is a project with that exact file, so if you do the same I did in the video, you should have the issue as well. Maybe you can confirm? @Louis_R :