You haven't posted the code for your disable_getopt_attribute function, but I guess it looks a little like this:

package My::App;

use Moose::Role;

# ... etc

sub disable_getopt_attribute {
  has("+$_", traits => ['NoGetopt']) for @_;
}
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And you're calling it like this from classes:

package My::Script;
use Moose;
with "My::App";
My::App::disable_getopt_attribute(qw/ foo bar /);
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Try changing the definition to this:

package My::App;

use Moose::Role;

# ... etc

sub disable_getopt_attribute {
  my $class = shift;
  my $has   = $class->can("has");
  $has->("+$_", traits => ['NoGetopt']) for @_;
}
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And calling it like this:

package My::Script;
use Moose;
with "My::App";
__PACKAGE__->disable_getopt_attribute(qw/ foo bar /);
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This way, the has function that gets called, is My::Script's copy of has; not My::App's copy of it.