You could try adding the following right at the top of your script. (Even add it before use strict - before everything else except perhaps the #! line.)

BEGIN {
    package Tie::Env::Warn;
    use Carp qw(cluck);
    use Tie::Hash;
    our @ISA = 'Tie::StdHash';
    sub STORE {
        my ($self, $key, $value) = @_;
        cluck "Modification of \$ENV{$key}!";
        $self->SUPER::STORE($key, $value);
    }
    tie %ENV, __PACKAGE__;
};
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That will print out a warning including a stack trace (which shows line numbers, etc) whenever %ENV values are assigned. If that doesn't help, then you could also try hooking the DELETE and CLEAR methods (the example above just hooks STORE).