Steps to reproduce:

1. Start Krita. Assuming auto-save is enabled (default);
2. Open some image
3. Select all
4. "Transform layer or selection" (Ctrl+T)
5. Tool options -> Warp
6. Tool options -> Anchor points -> Draw
7. Begin carefully placing and adjusting points

Expected:

The transform applies when I select other tool or press "Apply" button.

Actual:

Half-way though by anchor points adjustment, the filter applies spontaneously, abandoning all my points. Can't go back and resume moving anchor points. When this happens, I see saving progress flashing though status bar.

Workaround:

Settings->Configure Krita-> General -> Misc -> uncheck "Autosave every", then apply the transform, then check it again.