When a conflict exists in a pull request, a warning appears within the "Overview" tab with a link labeled "More Information". Clicking the link will bring up the "How to manually merge a pull request" dialog.

The 3rd step says to commit the changes and push using the following commands (replaced internal references with *):

git commit -m "Merge pull request #* from *-* to integration" --log --no-ff 
git push origin HEAD

I believe "--log --no-ff" should occur in the previous step, while using the merge command.