This is a Mac-only issue and it's present in earlier versions too (not just 9), though with rectangles it manifests itself less commonly in v8 than in v9. To solve the problem, use the option Method -> {"TransparentPolygonMesh" -> True} in Graphics to get rid of this problem. It will also disable antialiasing.
Posts with the same problem, appearing in a different form:
The reason why the mesh appears in those questions is that the polygons are transparent and they overlap slightly (by a pixel or so).
Test code:
g = Graphics[{Opacity[.5], Red, Rectangle[{0, 0}, {.5, 1}], Blue, Rectangle[{.5, 0}, {1, 1}]}] Magnify[#, 4] & /@ {Rasterize[g, "Image", ImageSize -> 50], Rasterize[Show[g, Method -> {"TransparentPolygonMesh" -> True}], "Image", ImageSize -> 50]} 
