so if he's magnetic, which he is because magneto can manipulate him, then it wouldn't have given back pictures of his innards
Magneto can manipulate aluminum and any metal which isn't magnetic, so Adamantium doesn't have to be magnetic.
Also, we're talking about him being in a place where they have a jet that size which has vertical take off abilities, a war-games room which can project images into solid objects and a machine which allows mutants with psychic abilities to locate other humans/mutants.
Who is to say the "MRI" they used isn't something different than the ones we actually use.