When I am downloading in bulk, say 100+ games, after the 20th game or so, freeshop will stop downloading the rest of the games in the queue. Another issue I experience is that when I start to delete the "installed" games in the queue, if a game is downloading, seemingly at random freeshop will just crash. Does anyone else experience these two bugs?
You're taxing the 3DS memory resources. Download less games per a single run session (under 20), exit out of freeShop, and download some more again. People will snicker at you for having hording issues, but if that's what you want to do with all the games available, shoot go for it.
I've crashed freeShop before doing exactly what you did when I was mass collecting Virtual Consoles. You should probably not stress freeShop downloading and deleting games at the same time. Only do one action at any given moment. Remember, doing both is telling the 3DS to read AND write data to the SD card at the same time. This is hard on the card and 3DS sd reader with its limited ~1.90 MB/s ?? transfer rate.