Steps to reproduce:

1. Put a simple satellite in a ~100km orbit.
2. Set up a maneuver about an hour in the future.
3. With auto-warp enabled, click "Execute Maneuver".
4. Wait for Mechjeb to start warping.
5. Uncheck the "Auto-warp" box while warping.
6. See that the warp level remains at the same level.
   At this point, unless you have enough time to manually reduce the warp, a different bug takes effect:
7. Since the auto-pilot is still engaged, after you warp past the node, it will drop out of warp and try to execute the node. But this is virtually guaranteed to be too late because it does not decelerate the warp gradually like it does when "Auto-warp" remains checked, and the game tick rate governs how far you overshoot.

I don't think this behavior is intentional. I know it cancels warp when you click "Abort", but I think it should also cancel warp when you uncheck autowarp. That way you do not risk hitting the bug in item (7), and is a more intuitive command. (cancelling autowarp should also cancel warp)