what seems to have happened is that you lost the tempo but by luck correctly guessed the incorrect timing the game asks of you. i just went back and listened to the song again and nope you are wrong. use this video:
I interpolated the cutscenes to 60 fps and recorded the boss footage using RPCS3.
youtu.be
go to the relevant part at around 9:10. the penultimate call and response has the call on the first beat of the bar starting at 9:13 and as expected, the response is on the first beat one bar later, at 9:16. then after that bar you have four bars with neither call or response, together with a long ritardando, and then the instruction for the final call and response comes at the first beat of the following bar at 9:36. if it were to follow the rules of the earlier calls and responses, the input from the player would be expected at the first beat of the next bar, at 9:42, but instead it comes halfway between the second and third beat of that bar, at 9:43.
indeed, there are some extra chimes there to show where the beat is, but they prove that i am right and you are wrong. those chimes play on beats 1 and 3 in both the bar of the call and on the bar of the response, and knowing that, you can clearly tell that the response comes in between the second and third beat of the bar with the response
just a bit about my background, i am not a professional musician or anything of the sort, but i played classical guitar for over a decade as a child and teenager, and I've been a choir singer for over 25 years. when i lived in the uk for one year i was a member of a bbc-affiliated choir, which was an absolutely top-tier choir, so i'm not completely useless as a singer and i have studied music theory in one form or another since i was 7.