Are they all achieved on the same character?
I think i remember this works on Kiwami and 2 but if you look at your character profile in the online data exchange you can see what achievements were gotten on that character to compare to your steam achievments if you missed something if you were using multiple characters.
If you have all other 49 achievements/trophies on 1 character in the your character profile then something is up.

Ok I will look there later today. I only have one character so I think that I should have everything. Maybe an achievement popped on steam but I didn't save.

@JKthree Thanks for your help. I am over 300 hours in and I am just realizing that steam achievements and in game medals are different... I wish they were all achievements it is just kind of confusing...

Edit: I think the medals are broken... not necessarily the trophy. I just printed out a list of all of the trophies and checked off the ones it says I have in game. I have cleared the game completely, collected every mitama, have multiple mitama at max level have over 190 missions cleared with knives yet all of these medals are not checked off. I don't even know how I would get them to be checked off as they are already completed. Anybody have any ideas?

I'm also like you. I haven't unlocked the last trophy, and I think it's a serious bug

oh，i have an idea。You can talk to 【Yamato】，click the 【guide】, and then you can unlock it. That's how I unlocked it