Have you tried reloading a save and killing him again? I know Bethesda did a CRAPPY JOB with the amount of glitches you can get fighting miraak. Last time I fought him not only did he stay in ghost form when I brought his health down but one of the dragons WASNT THERE! And so it become a nightmare trying to just kill the dragons in just the right sequence so his health would regernate fully all three times so I could finally kill him for good. It was so bad trying to figure out how to give him more health from the dragons (if all 3 were there I could just kill all of them before even engaging miraak but since once wasn't physically there miraak would still try to absorb the non existent dragons soul when his health was low) so I could finally ended it. I even switched the difficulty down from legendary to novice since I was getting so angry I just wanted to rinse and repeat the process as quickly as possible so I could finish the stupid quest.
My view of Bethesda dropped tremendously after that experience. We all know glitches will always be in games like this and some will be frustrating but to have that many that break a MAIN QUEST and...RIGHT AT THE climix is absolutely inexcusable...so...I feel your pain...
But I've never experienced that one yet. Miraak wasn't even on the tentacle when he came out after that nightmare above. He was just flostibg half a mile away from Mora's tentacle but luckily he still died at the end otherwise I would of busted the TV.
So my only advise is reload a save and try again or find a solution online.