I was having the same issue on my Nexus 6P with Marshmallow, and I believe I just finally fixed it after spending a bunch of time and scouring the internets with no luck!
I'm trying to download PDFs which are behind a pay wall. I believe the issue is that there is some sort of redirect to verify that you have access to the file, so the link is not actually a PDF. On my old phone, a Galaxy S5, Chrome would ask me if I wanted to download the file (which works) or open it with my default PDF viewer (which never worked). On Marshmallow, Chrome always chooses to open the file with Drive PDF viewer, which is not even my default PDF viewer! Maybe I had set it as the default at some point. I can't remember. Regardless, there were no defaults to clear in the app settings for Drive, and clearing the defaults for Chrome didn't help, so I was at a loss trying to figure out how to fix it, but it looks like I just did.
Here are the steps.
- Go to Settings > Apps > Drive.
- Disable Drive. It may ask you if you want to replace it with the stock version. Say yes.
- Open up Chrome and try to download the offending PDF again. It should ask you if you want to open it with Chrome or if you want to open it with another PDF viewer that you may have installed, such as Acrobat.
- Select Chrome, and tell it to Always open it with Chrome. It should now download the file, and will always download PDF files in the future instead of trying to automatically open them.
- Go back to Settings > Apps > Drive and re-enable Drive.
You should now be able to tap the downloaded PDF in your notification bar and open it with Drive or Acrobat or whatever your favorite PDF viewer is. It should be safe to set it as the default PDF viewer here, as this is a different default than the one used for downloading PDFs from Chrome.
EDIT:
You didn't say whether or not Chrome was trying to open the file in Drive or some other app, so I just assumed Drive, since that's what it was doing with mine. Drive would pop up briefly, and then go back to Chrome, and say there was an error. If it is trying to open some other app, try uninstalling, then reinstalling that app, replacing it with Drive in the steps above.