a "set object polygon..." object has a point that is outside the axis cropping boundary, that point is ignored, which is incorrect. Such points should be rendered on the cropping boundary (or rendered outside the cropping boundary, and the resulting outline and fill pattern cropped correctly) rather than ignored. That is important (e.g.) for filled polygons that are meant to extend fill all the way to the boundary of the plot; with the current system, such polgons must be tediously hand-fitted to the boundaries of the plot, which may or may not be known in advance.
I cannot reproduce this problem.
Please provide an example script that demonstrates a clipping failure.
Be sure to specify what terminal you are using and what version of gnuplot is failing.