title: Git sees to many changes within branches while making pull request
body: <p>While working on a project we have faced a problem with git.
  I have a branch "D", which is a feature branch. 
  Then I have a branch "A" which is my master.</p>
  
  <p>I have merged <code>"A"</code> into <code>"D"</code> but git sends me a message: "Already up to date" when there are some changes at the "D" branch. </p>
  
  <p>When I was creating branches, every next one depends on the previous one. So the flow was like <code>A -&gt; B -&gt; C -&gt; D</code>.
  Since branch "C" I can see on my pull request that 46 files are changed while only 4 to 5 files were changed. </p>
  
  <p>I think it's important to mention that while I was working on Ubuntu and there were some problems with files permissions and I did <code>sudo chown</code> command on some files. </p>
  
  <p>While doing <code>git fsck --full</code> I can see the output:</p>
  
  <pre><code>Checking object directories: 100% (256/256), done.
  Checking objects: 100% (1072/1072), done.
  dangling tree 1c706090df93f04b78e35d94ef9a55af86daa444
  </code></pre>