The are trying to make it look like Annie killed Stuart again

I still think it was Adam cause Annie has all the reason in the world to want to cover that up. Remember Emma said to Adam, "You know Mommy didn't shoot Stuart" which indicates Adam knows the shooter and it wasn't Annie. Also, it could have been little A, he was there that night too or far-fetched as it might be it could be Emma. Those are the only three people it makes sense that Annie would be trying to protect. She has vested interest in Adam and until her name is cleared she needs him on her side.

I think from Adam's reaction today from his flashback as well as what Emma said to Adam a couple of weeks ago, that Adam did it accidentally, thinking Stuart was an intruder (or maybe aiming at Zack or somebody and hitting Stuart by mistake). I think Annie and Emma saw the whole thing.