I’m using KDE and have noticed the same issue for a while now. I’ve played with the themes and settings just as mentioned here. The only thing I’ve found that ‘fixes’ it is to remove the google-chrome folder from ~/.config, which restores the correct colors. But if I close Chrome and open it again, even without signing into anything, it goes back to following Manjaro system colors.
Another thing that I have noticed that might be linked to the whole thing is that my mouse cursor has changed? I get the default manjaro mouse cursor while I move my cursor within google-chrome, but when I move it outside, I get DMZ-Black, which I have set up in my system configuration. Just for chrome it seems to be ignored.