well, try to find which pages don't server the exact same JS-file, once you have identified that you can see what the differences between those are (cfr. the approach taken in this post from earlier today) and exclude accordingly.
alternatively you could disable inline JS from being aggregated, which will 99,99999% sure solve this in one swift swoop (but which will exclude all inline JS from being aggregated) by adding something like this in a plugin or a (child) theme's functions.php;
add_filter('autoptimize_js_include_inline','pixeldynamo_ao_js_include_inline',10,1);
function pixeldynamo_ao_js_include_inline() {
return false;
}
frank