It looks like the problem with youth teams showing different logos is still here, and it doesn't look like an easy fix.
Take Swansea City.
Their senior team is ID: 724 and shows the correct logo:
The u23 squad has a separate ID: 2000146179. They show a logo for a 5th tier Polish side called LKS Barycz Sułów, a team which doesn't exist in the database. I checked the logopack and indeed the entry exists:
Similarly with the u18 squad with ID: 2000146181 having an image for a club called WKS Wierzbice, again a Polish club not in the game's database:
I think one of a number of things may have happened here:
Your image bank has been built over a long period of time, and in the years since it was started some of the clubs from older games were entirely deleted from the official database, and the numbers have been reassigned in England in line with changes in the English youth system (when the reserve league ended and the u23 league began). I think this is unlikely, as I don't believe SI ever reassign ID numbers. The database has a system for making clubs defunct, as can be seen in some player histories for former teams that have recently dissolved.
One of your contributors has been playing with a save at some point with an extended database for Polish lower leagues that added in new clubs, and has not realised that the ID numbers they provided did not match the vanilla database.
Option 2 is almost certainly the case, because the IDs are assigned to youth teams not as part of the database, but at the start of each save and is impacted by which IDs are available at that point. Here is the Swansea City u23 squad in a different save with different leagues loaded and a database that includes Scottish lower league expansion (that would not have impacted Swansea):
As you can see, the ID number of 2000147423 is different. The main Swansea City squad however has exactly the same number as before.
Sorry for the long post, but the reason for this happening was bugging me and I wanted to understand it for myself, and wanted to share my findings with you. There is unfortunately no easy fix for what you've built so far. My only advice would be to create a thread where people can tell you the ID of youth teams in their saves with incorrect logos (as the team name alone will be insufficient), for you to manually remove that ID from the logo config file and then move the graphic to a personal archive in case of future need to reduce the download filesize, or otherwise an archive folder in the download. The config file would be the most important thing as even if people don't delete all of the graphics for a fresh download, each update pack will overwrite the config file to 'hide' those incorrect images.
Going forward, your solution would have to be manually checking the database to make sure the ID number given to you by contributors is valid for the vanilla database and not the result of an editor data expansion. As you have a working relation with sortitoutsi, I'd recommend their database checker as a quicker alternative to the official pre-game editor: https://sortitoutsi.net/search/database
I hope this monster post is of help!