You only need to pick them up (I think) in level 2, with the big blue stone blocking the exit. Make sure you get the one before you zipline down otherwise you'll have to restart.

First Steps
You'll just get this achievement by walking through the level.

Prologue Complete
Popped shortly after exiting the sewer.

They
Popped shortly after using the zip line and seeing the small cut scene about the hunters. I read the note but I'm not sure that mattered.

Make sure to pick up the mystic stones!

Uncharaccoonofus
Popped after I used the zip line.

DON'T DO IT, I HATE WATER
I jumped in the pool behind the house (on the way to a mystic stone)

House Complete
Popped shortly after starting the level.

A Different Way
I went up the path on the right, up a hill. It's following a path of mystic stones.

Just Another Step
I went to the right shortly after entering the level and walked through a bush. Check out Kitt's awesome video which shows the exact location.


???
Popped as I walked through the pathway between the stone walls.

Secret #1-3
Popped shortly after starting Level 5.

A Photo?
Popped about 10 seconds after Secrets #1-3

Dev Happy
Popped shortly after the start of the level.

The Truth
Popped a little ways further along the path, closer to the tree.

Special Secret
Popped under the tree.