The logos in the game are in .oi format to prevent licensed logos from being manipulated. The community has converted them to .png files, so maybe that will help. The format for OOTP to see the logo is city_teamname.png It is possible the logos have years tagged at the end of the file names though and since you have teams out of their time they are not getting read. I'd take these .png logos from the link, drop them in the logos folder, and then manually assign the logos from the Team Settings Screen. Post here again if you are unsure of any of those steps and someone can help.
Logo folder can be found by going to Settings from Start Screen, Troubleshooting tab on the pop-up, and then "open folder with customizable data" button.
https://www.mediafire.com/file_premi...Logos.zip/file