First, I apologize for not digging through forums posts in the chance this has already been covered; there are just too many b*&^% threads about MM to sort through.
I noticed in the pre-game setup, not all skulls for Halo CE are available. For example, Boom skull. I picked it up “Halo” and even have the achievement for it unlocked, but this skull is not available to use.
Hmm haven’t noticed i will try pick up in other halo then
I also noticed another oddity about it.
In Halo CE Anniversary: There are 14 skulls
In MCC, Halo CE Anniversary, I only have 10 skulls available to use. I’ll get a list later.
Some of the Skulls, like Boom, are pre-order only for now. They will be unlocked for everyone at some point. From memory, it was arouns the start of December. If you did pre-order and Boom was the skull you were supposed to get, make sure that you either redeemed the code for it, or that it was downloaded along with your digital purchase 
I posted something the other day wondering if you can only use certain skulls in CE because some of the ones I was collecting aren’t showing up as being able to be used. If it’s a glitch, hopefully it will be corrected with the update on Wednesday. Otherwise, hopefully they will be unlocked soon.
> 2533274813317074;4:
> Some of the Skulls, like Boom, are pre-order only for now. They will be unlocked for everyone at some point. From memory, it was arouns the start of December. If you did pre-order and Boom was the skull you were supposed to get, make sure that you either redeemed the code for it, or that it was downloaded along with your digital purchase
Problem, Boom isn’t a preorder bonus skull though. It is unlocked on the second Halo Combat Evolved Anniversary map “Halo”. It is the third skull in the game, located above the first tunnel by the first Marine group to be rescued. Picked it up, unlocked the achievment, but don’t have for use. In Halo CE Anv, the only skull not found in the anniversary campaign is Grunt Funeral, that was a pre-order skull back in 2011.