Tone, I'm pretty sure this is happening because you're expecting the new waypoint to be created in exactly the same position as the centre of the turningpoint box. This isn't the case; it'll be created in the position of the mouse cursor which is likely off by a few pixels, which will translate to a few seconds of accuracy.
Thanks for bringing it to my attention though. In the future it might be possible to detect the case where you're clicking on an existing turningpoint and enforce the exact position of the turningpoint, rather than getting the current mouse cursor position.