I don't believe this is a bug. When you call a high-level plotting function like plot or plot3, MATLAB needs to know how to configure the axes into which the graphics object will be plotted. By default, "new plots added to the axes clear existing plots and reset all axes properties." [That's not technically true; the Position and Units properties keep their values.]
To avoid this behavior, use the hold function to change the behavior from the default behavior I described above, use a lower-level plotting function like line, or manually change the axes NextPlot property (which is similar or equivalent to what hold does.)
I'm guessing you didn't see this behavior when you called plot because you also used hold or because you set the ButtonDownFcn property after plotting.
