On turn 16 do you not have the unkillable buff because Ninja has his go too early and the buff is removed?  Ninja is a difficult character to speed tune because of his A1 and the turn meter boost that he receives.  Have you maxed out his skills so he has the same cooldowns as deadwood's calculator?  The reason being is because it will assume maximum cooldowns which in turn impacts when Ninja does his A1's, and thus when he gains turn meter. 

If that's the case then I would recommend trying to remove 1 speed from Ninja and seeing how it goes.  I had to do this for my current unkillable team where Demytha was slightly out of tune with CB and I added 1 speed to her which got it perfect.  The issue is that speed isn't an integer value as far as I know, so you could be slightly over if Ninja is too fast

From what I saw the unkillable buff wasn't on the whole team. Which means the slow Maneater didn't get his turn at the end of turn 15. I will run it again and try to see what is going on. 

You may need to play with delays on Ninja and the ME's.  Its been awhile since I used double ME with Ninja for a CB team but I remember that being part of it.  Because he self turn meter boosts with one skill (cant remember which off the top of my head) you need to mess with delays to get it just right.  I also believe I had faster ME delay unkillable 1 turn and the slower delayed it by 3.  Manual the fight for the first 4(?) turns and then you were golden on auto.  

Can you share your Ninja build and masteries? This is easy double maneater, correct?  How many times have you run it and had this issue? Were you hitting affinity? Cause weak hits ruin Ninja's TM boost on his A1. Do you have Ninja's skills prioritized as in DWJ's vid?

Ninja looks a tad fast, maybe by 1 or so. Tough to say for sure.

If you can get a video of turn 15-16 that would help too. :)