On the second level jungle rollers there is a gray box with an exclamation..

I miss those three as well, but I know why.
In the third warp room there is a level called The Lost City. Finish that level without dying, and get all the boxes (involves a LOT of backtracking) and you have it.

Now try that level again and lets see how many boxes you miss!!

P.S.
There is this other level called Castle Machinery-if you go on the green gem, you finish the level and get 26 lives! The green gem is important!

You have to get a colour gem on the level jaws of darkness. Which is hard. It got me stumped for ages.

Sorry, I may have said the wrong answer its the lost city not jaws of Darkness. Now thats even harder, I don't backtrack I just make sure I don't die. Good luck

To get The Green Gem You Must Complete level The Lost City Without Die With All The Boxes Want More Guides ? Follow This :
Level : The Lost City
The Gem : Green Gem
No Required Gem
Boxes : 26
Difficulty : Hard

Complete The Lost City With All Boxes Without Dying

The Green Gem Had Be Must Getting At The Lost City (Once You Must Complete The Level Without Dying) And Go Back To The Level And Had The Green Gem!

So I dunno if I'm doing it wrong, but if you approach the wall of boxes right after the checkpoint from as far left as possible, you can hold X and forward to break the top left box. After that, you can jump on the left most column (now only two boxes) without breaking them. If you jump on it, you'll fall, but if you jump on it and continue to run forward, crash will run in place on top of the box. You can then jump forward again to land on a tiny ledge over the wall of boxes. From here, you can jump backwards diagonally to the right (hold back and right) and land on the silver crate (which is actually a jump crate, not an exclamation mark crate). There are three boxes located SOMEWHERE in the space above said crate. I can only ever consistently get two, the third one is trickier. (there's two to the right that you can get by holding X while jumping on the box and going right at the height of the jump, and one somewhere on the left. The left one is the difficult one).