See https://gist.github.com/peti/ed64f5a9ac193690ec10 for an easily reproducible test case. Basically, the command

$ stack --nix build stack-bug
$ stack --nix exec stack-bug
[]

executes the stack-bug command without any arguments -- like you'd expect. The command

$ stack --nix exec stack-bug --
["--extra-lib-dirs=/nix/store/j1q555xv31177kg9ncc9y0p3xaqbq1gf-ghc-7.10.2/lib","--extra-include-dirs=/nix/store/j1q555xv31177kg9ncc9y0p3xaqbq1gf-ghc-7.10.2/include"]

however, does not. Instead, it adds additional flags that look like they're intended for cabal configure.

This means that it's basically impossible to pass command line options to programs executed via stack --nix exec ....