Is it possible that a set of functionally related proteins in a pathway fulfill different functions?
If Y can be seen as the inverse or absence of X function, it sounds to me like an incoherent type 3 feed-forward loop, where
A activates B
B activates C
A inhibits/reverses C

example from literature, E.coli: fnr as A, and arcA as B, cydAB as C
source: http://www.pnas.org/content/100/21/11980.long