When Sam and Dean locked Lucifer back in his cage at the end of season 5, they also trapped Michael in the cage with him, however when Crowley and Rowena arrange for Sam's meeting with Lucifer without actually opening the cage, Lucifer is in there by himself and Michael is nowhere to be found, despite even being mentioned as recently as season 10 when it was said he and Adam are still trapped in the cage with Lucifer.
In season 5, when Lucifer fell into the cage, he was wearing Sam as a vessel. Also the decaying of the original vessel was already advanced. No explanation is offered as to why he is appearing with this human form, instead of his true form.
Tween Amara and teen Amara they had bright blue eyes, but adult Amara clearly has brown eyes.