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I wrote a simple reproducer program; it can be acquired here: https://github.com/jgfouca/f90_dep_bug

The broken file contains:

module ice_flux

  implicit none
  save

  real, dimension (1,2,3) :: &
       daidtd  , &
       dvidtd

  ! The presence of this segment breaks the detection of the ice_state dependency
  real, dimension(1,2,3) :: &
#ifdef FOO
       baz, &
#endif
#ifdef BAR
       bla, &
#endif
       goo
  ! end broken segment

contains

  subroutine init_history_dyn
    use ice_state, only: aice, vice

    daidtd  (:,:,:) = aice(:,:,:)
    dvidtd  (:,:,:) = vice(:,:,:)

  end subroutine init_history_dyn

end module ice_flux

With this code, the dependency on ice_state is missed. If either (or both) of the FOO or BAR ifdefs are removed, the dependency is found. If the 'use ice_state' statement is moved to before the ifdefs, the dependency is found.

This issue looks somewhat similar to #18188 but is a bit different since the ifdefs are removed from the use statement.