This is happening to me now with 2.5.7. I also converted the whole site to https using LetsEncrypt, so I'm not sure if it was the MODX upgrade, the SSL conversion, or something else.
There is still the question of where the SEO people are finding the index.php links. There should be no such links on the site.
Fire up PhpMyAdmin, select the database, and on the SQL tab, try these three queries:
SELECT * FROM `modx_site_content` WHERE content LIKE "%index.php?id=%"
SELECT * FROM `modx_site_htmlsnippets` WHERE snippet LIKE "%index.php?id=%"
SELECT * FROM `modx_site_templates` WHERE content LIKE "%index.php?id=%"
The spacing in the LIKE clause in the queries above is most common, but if you have any SEO reports that give the index.php URL, duplicate their spacing in the LIKE clause.
If you find any, you can correct them to proper link tags like the one below <a href="[[~12]]"> right there by editing the content or snippet field and clicking on "Go".
or
<a href="[[~12? &scheme=`full`]]">