I have some experience with film permits. Permits are required when filming for any commercial or non-personal use. Students, non-profits, etc. can often get a film permit free of charge.
When you sign for the permit, you state where you will film and what you will film.
The parks are protecting themselves from liability and limiting the damage to the park that a film crew/set can cause.
So, if they did not secure permits beforehand, is it legal for average tourists who take beautiful nature photos in national parks to have them sold on sites like Webshots? Does that not become commercial use?
Soooo....when that bear jumps outta the trees, and I don't have a permit to film a BEAR, I'm illegal? /sarcasm.....sorry, but, I want my America back.