remove-modxminify-duplicates.php

<?php
$modxminify = $modx->getService('modxminify','modxMinify', MODX_CORE_PATH . 'components/modxminify/model/modxminify/',[]);

$files = $modx->getCollection('modxMinifyFile');

$list = [];

foreach ($files as $file) {
    if (empty($list[$file->group]) || !in_array($file->filename, $list[$file->group])) {
        echo $file->filename . '<br>';
        $list[$file->group][] = $file->filename;
    } else {
        $file->remove();
    }
}