Sometimes in Mathematica denominators are not in the form you might expect.
We can use FullForm to see how Mathematica represents your expression internally
d1= U/((a - b - c) (a + b - c) (a - b +c) (a + b + c));
FullForm[d1]
which shows us that Mathematica sees this internally in this form:
Times[
Power[Plus[a,Times[-1,b],Times[-1,c]],-1],
Power[Plus[a,b,Times[-1,c]],-1],
Power[Plus[a,Times[-1,b],c],-1],
Power[Plus[a,b,c],-1],
U]
So, since Mathematica has this is in the form of U*stuff, here is one way you can do this
d1/.U*stuff_->U/(-4*S^2)
which returns the result that you wanted
-U/(4 S^2)