I don't think it's anything to do with your particular workflow - this feature currently just doesn't work. I've had it work in the past, but in the current CC apps (InDesign is my PDF source), it either crashes or fails to complete in the manner you describe.
Greetings! I am sorry to hear that you are facing issues with compare feature. Please try out the files in our new and improved Compare functionality in the latest version of Acrobat DC Pro. Latest version for Adobe Acrobat DC build number: 2015.020.20039 (Continuous).
Reach out to us in case, you face any issues. Also, you may log a Bug Report at: Adobe Acrobat - Feature Request/Bug Report Form
Adobe Acrobat DC Team.
Also for future readers. I have found that the compare can also fail depending on the program that created the PDF(s) being compared. If this is happening to you the correction is to re-generate the PDF(s) using the Adobe PDF printing process and then compare the resulting versions.
This solved the error when I was getting it even on the latest build of Adobe Acrobat Pro DC.