To my knowledge, this can only occur when a reference is passed between two separate instances of the Perl Interpreter running within the same process

All it takes is an inappropriate SvREFCNT_dec() in XS code to generate the error:

use warnings;
use Inline C => Config => BUILD_NOISY => 1;

use Inline C => <<'EOC';

SV * foo() {
     SV * y = newSViv(42);
     SvREFCNT_dec(y);
     return y;
}

EOC

foo();
[download]

Cheers,
Rob