After Abomination was beaten by Hulk in The Incredible Hulk, we never heard about him. So, it's safe to assume that S.H.I.E.L.D. took him in custody somewhere classified.
But now
S.H.I.E.L.D. is out of commission. Also, in Marvel's Agents of S.H.I.E.L.D., it is shown that the Fridge had fallen, freeing all supernaturals locked in there.
Can we assume that Abomination is also free now? Or is there any glitch with this assumption?
No, the Abomination was not in SHIELD custody.
The Marvel One-Shots short film The Consultant clearly shows that the Abomination is in the custody of the US military. The short is about keeping it that way and making sure the Abomination doesn't get handed over to SHIELD.
If the Abomination is loose following the Hydra events, it's due to parallel action in the US military which we haven't seen or been told about... so as of now I'm going to assume it hasn't happened.
In the Agents of SHIELD episode T.R.A.C.K.S. (S01E13) Coulson tells Ward
What you're doing is against protocol, so if you endanger an operation or if anyone gets hurt, I'll reassign you to Barrow, Alaska, and you'll spend the rest of your years pulling the night shift guarding Blonsky's cryo-cell.
So, Abomination IS in S.H.I.E.L.D. custody! I was rewatching season 1 when I stumbled onto it and that's what made me look it up but nobody seems to know that.
