Was trying to combine a bunch of pdfs into one file. One kept coming up with a little yellow exclamation mark in the corner. When I clicked on it, the program told me "cannot open this file."
I then analysed the file using Adobe Acrobat's own analysis functions, found nothing wrong with it.
I'm putting this up for anyone else who runs into this problem! I found the answer.
Turns out there was a question mark in the filename for that particular file. That's fine for Mac OS, you can have all sorts of characters in the names of files, but unfortunately the Adobe Acrobat program does not recognise a filename with anything other than a-z, A-Z, 0-9, and perhaps - . ( ) etc.
Solution - rename the file in the finder without the offending character!