No, you're not wrong. It's just that I find
replace ___ with ___ a little more awkward in a question because the object of
with is fronted to become the question word. On the other hand, the object of
for in
substitute ___ for ___ is conveniently where it "should" be.
What do we replace X with?
vs.
What do we substitute for X?
(I think you know already that
replace X with Y is
substitute Y for X.)
CJ