I haven't ordered any in years, but from your description, I'd agree that you got the wrong size.
When I was laying my track, 25 years ago, they didn't have the code 40 joiners, so I used code 55 joiners on the code 40 track. Even then, I didn't have to file them down, as long as I had reasonable flanges. Pizza cutters didn't like them, but I'd already gotten rid of most of those.