This game has quite a few invisible item boxes hidden throughout most of the stages.
To open them you have to get close enough to hit them with your character's melee attack
(or hit them with anything that does the same type of damage, like the Komainu / jumping dog statue)

The first box containing some food is on the small island in the pond after the first batch of skelletons.
Unfortunately only Ikazuchi and Ame-no-Uzume can reach this one, as far as I know.

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A box containing a bomb is in this circle of sacred rocks(?) just before the bridge leading to the boss of Stage 1.

Stage 2 has a box right at the start just before the bridge. This has a Komainu inside.

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A Bomb item is hidden behind the trees all the way in the corner just before the shrine ruins.

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There is a 1-UP inside the ruined shrine building after the big Oni guy

A barrier charm is waiting to be collected in this small hut in Stage 3.
And another 1-UP was left behind just past that.

Another bomb waiting to be picked up in this dead end path in the underworld.
Be wary of hands, that fall down on that exact spot.

Yet another bomb was left behind at the end of the 2nd airship.

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A cup of tea was abandoned on the airship that crashes into it's allies...

Since Stage 6 is pretty much only a boss we can skip ahead to the castle.

There is a 1-UP hidden in this secret room, past the 3rd fire machine and hands

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And another 1-UP at the end of the spikeball corridor

That's all of the secret boxes.
Good luck and have fun :3