Problem

If you create a branch off of master, make some commits and then create a pull request from the new branch back to master, initially in pull request creation page, you can see the diff and it is correct. Once the pull request is made you cannot see the diff. 

Once you merge the pull request, no merge commit is actually made. Furthermore, the master branch does not update with the new commits even though the pull request is marked as merged. No errors will occur in the logs. 

Cause

A setting in the .gitconfig file on the Bitbucket Server instance :

[branch]
autosetupmerge = always
[branch "master"]
mergeoptions = --no-commit --no-ff

This option stops the merge on master.

This configuration is typically set to prevent people from committing and pushing directly to the master. 

Resolution

You can remove this configuration from the ~/.gitconfig file in your home folder. This is where all --global settings are saved.