After a recent play through I came across this issue:
https://steamcommunity.com/app/203160/discussions/0/846960628526736106/
(just for the record it is a bug)
It starts around here:
https://youtu.be/Onpwqdmul9w?t=59

On boat the successive quick time
events do not appear during the boss
battle (the boss needs to be killed
via quick time events)

Could be v-sync related...
Do not set v-sync related settings
in nvdia inpsector (keep defaults)

use game settings:
refresh rate 50hz
v-sync double buffer
fullscreen on
exclusive fullscreen on

other wise it could be win 10 related
on windows 7 the quick time prompts
do appear.

last resort use a save file....
that is made just after the boss battle
but you will loose the specific progress
made up to that point.