Recently at a special MARVEL event, The Inhumans movie has been announced for 2018. Just before [Avengers: Infinity War - Part II](movie:2390833). Now most comic readers know that they were Kree experiments on humans that developed their own culture outside of humanity in the Himalayan Mountains. Now, in the MCU they have changed numerous villains origins like Crossbones, Iron Monger, Mandarin, and Arnim Zola (robot style). Now they could easily change it according to already established origins.
[The Inhumans](movie:910490) don't have to be Kree experiments from a looooooong time ago, they can be recent and human experiments. They even mentioned what kind of experiments in Captain America: The Winter Soldier.
That's right, Baron Von Strucker created our MCUs Inhumans. Inhumans-Miracles, same thing. If they just keep the Miracles to just Quicksilver and Scarlet Witch, it wouldn't make sense especially since he said "The age of" which means that there are a lot more Miracles. They also never did specify that Miracles are mutants. He could have said something like, "Aah Miracles, the next step in the human genome" we would know that they are mutants and that's it. But there was no confirmation of that sort. No point out of what is what. Just because it starts with an "M" doesn't mean anything.
HYDRA has already been a major contributor to what happens in the MCU. Thanks to Captain America: The First Avenger, The Avengers, [Captain America: The Winter Soldier](movie:254973), Agents of SHIELD and soon to be The Avengers: Age of Ultron, and Agent Carter. Why can't they contribute past that? We definitely know that HYDRA will have a major effect on Captain America: Civil War and probably Black Panther, Captain Marvel, Ant-Man, and Doctor Strange (as he was mentioned and called a threat by Agent Sitwell in Captain America: The Winter Soldier). The effect the Red Skull has had is immense. If he has affected all those movies and might affect more, why not Inhumans?
Now HYDRA made a careless mistake, they buried the bodies so far that even their souls cannot find them. Now HYDRA aren't the kind of people to grab the ol' rusty shovel and dig up an ol' hole, they would put them deeeep into their facilities. Now, a lot of these Miracles probably could come back to life (as they are Miracles) and maybe one of them could help them escape with their new found powers (eg Gorgons strength and Black Bolts sonic scream) then they would get away and make their own secret civilization to hide from HYDRA and from the rest of the world because they are scared to show what they are.