There are ways to get secret scrolls on every battle stage:
(I only know a few)
Tanzaku Town- Hit the slot machine outside Panchinko Parlour about 10 times.
Spider Forest- Attack the spiderlings about 10 times.
Moonlit fields- Attack the coffin about 10 times.
Forest of death- When you see a rainbow appear above the river, stay in it for 4 counts.
Ichraku Ramen- Break everything.
Konoha Forest- Climb the tree for a certain amount of time.
There are others, but I can't remember them. When you play the Leaf Story slot machine in Tanzaku town, try to play through the Naruto minigame. If you get through the whole thing, you'll get a scroll with a hint about the hidden scrolls. (There are ten hint scrolls in total)