Sorry for not releasing an statement earlier, thanks to the info you guys provided we were able to find a cause for this and have prepared a fix.
We haven't been able to reproduce the issue so far, but we are confident this will fix the trophy issue.
Also, We can't provide an ETA for the patch as of now, but will update whenever we get that info.
EDIT: The patch has been published for both PS4 EU and US Regions.