STL does not support any units, the number in graphics are just converted to numbers. So these numbers can be interpreted as kilometers, meters, millimeters, lightyears, Plancklengths et cetera... Either you scale them in e.g. millimeters (what is commonly used in CAD), or tell the CAD software that the number it reads should be interpreted as e.g. millimeters...
You can use Scale to scale everything:
Scale[Sphere[{0.5, 0.5, 0.5}, 0.050], 1000, {0, 0, 0}] (* all units in meters, then converted to millimeter *)
Graphics3D[%, Boxed -> True, Axes -> True]
Export["out.stl", %]
Show[Import["out.stl"], Boxed -> True, Axes -> True]
Shows that the STL file indeed is now scaled to millimeters