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The point is there -- it's simply lurking behind the contour plot. Or, in matplotlib jargon (one of the plotting packages Sage uses is called matplotlib), it doesn't have a higher zorder. The zorder is the layer level, where the layers are drawn from lower to higher.

I can never remember what zorders different things default to, but it's usually easily changed manually:

var('x,y')
f(x,y)=sin(x)*cos(y)
G = contour_plot(f(x,y),(x,-3,3),(y,-3,3),contours=20,plot_points=100)
G += point((1,1), size=100,zorder=2)
G.show()

produces