1. What happened
I tried to merge a scene using UnityYAMLMerge set up in git as per http://docs.unity3d.com/Manual/SmartMerge.html and got the following result
$ git mergetool --tool=unityyamlmerge Assets/Scenes/Boardgame.unity
Merging:
Assets/Scenes/Boardgame.unity

Normal merge conflict for 'Assets/Scenes/Boardgame.unity':
{local}: modified file
{remote}: modified file
/usr/local/Cellar/git/2.4.2/libexec/git-core/git-mergetool--lib: line 130: 6881 Segmentation fault: 11 '/Applications/Unity/Unity.app/Contents/Tools/UnityYAMLMerge' merge -p $BASE $REMOTE $LOCAL $MERGED
Assets/Scenes/Boardgame.unity seems unchanged.
Was the merge successful? [y/n]

Your tool is causing git mergetool to crash

2. How we can reproduce it using the example you attached

Try to merge any scene in git using git mergetool

This is the exact same bug people are having in the first comment on the blog here:
http://blogs.unity3d.com/2015/06/02/how-we-do-fast-and-efficient-yaml-merging/