Maybe this is what you want?

scale = 0.1; p1 = ListPlot[{{-0.4, -0.24}}, PlotStyle -> {GrayLevel[0.4], PointSize[0.09]}]; p2 = Graphics[{GrayLevel[0.4], Ellipsoid[{0.9, 0.6}, {3, 2} scale]}]; Show[{p1, p2}, PlotRange -> All, ImageSize -> 300] 

You have to scale / rescale the ellipsoid, not the total graphics!

Maybe this is what you want?

scale = 0.1; p1 = ListPlot[{{-0.4, -0.24}}, PlotStyle -> {GrayLevel[0.4], PointSize[0.09]}]; p2 = Graphics[{GrayLevel[0.4], Ellipsoid[{0.9, 0.6}, {3, 2} scale]}]; Show[{p1, p2}, PlotRange -> All, ImageSize -> 300] 

You have to scale / rescale the ellipsoid, not the total graphics!

And it might be useful to specify PlotRange and PlotRangePadding:

Grid[{Table[ Graphics[{GrayLevel[0.4], Ellipsoid[{0.9, 0.6}, {3, 2} scale]}, PlotRange -> {{-0.5, 2}, {-0.5, 2}}, PlotRangePadding -> 0.5, Axes -> True], {scale, 0.1, 0.5, 0.1}]}]