How to prevent Google Scholar from merging two different papers?
[Update: Multiple users have reported that this doesn't work.] 


Go to your Google Scholar profile and bring up the add article dropdown, click on "Configure article updates": 
Select the radio button for "Don't automatically update my profile" and click the "Update settings" button: 
When Scholar wants to merge your papers, instead of going ahead it will send an email to ask if that is the correct course of action.