Yes, unfortunately this is a common problem and it happened to me as well. The reason why is because RetroArch uses an internal database to "verify" your ROM's. So when it's searching thru your folders, it doesn't actually look at the "filename" but instead it does a "CRC" check and then compares that value to see if it corresponds to one that's in the database. If it finds a match then it will know exactly what ROM that is and it will add it to your playlist along with all the info.
The only way to workaround this is to edit your playlists manually, or to use one of the playlist builder apps floating around. I actually ended up making a batch script to build my playlists, but I did test out these two Playlist Builders and they both seem to work pretty well.
Playlist Buddy
Playlist Manager
I would suggest downloading both of them and playing around with both and decide for yourself. I didn't really spend a lot of time testing them out because like I said before, I ended up just making a batch script to build my playlists.
And when you add thumbnails to RetroArch, they have to be added to a specific folder structure that corresponds to your playlist, and the filename of the "thumbnail" image, needs to be exactly the same as the filename of the "ROM".
For example: Zelda, Ocarina of Time
This ROM is located on my SD Card at...
/Games/Nintendo 64/Legend of Zelda, The - Ocarina of Time.z64
The thumbnail image is located on my SD Card at...
retroarch/thumbnails/Nintendo - Nintendo 64/Named_Boxarts/Legend of Zelda, The - Ocarina of Time.png
The thumbnail has to have the EXACT same filename as the ROM.
And one other little issue that you MIGHT run into, if you have ROM's that have a filename that contains a
& character, then you have to use an underscore in the "thumbnail" filename instead.
Example..
ROM: Toejam
& Earl.gen
Thumbnail: Toejam
_ Earl.gen
Hope that helps! Let me know if you have any other questions.