I investigated the image images/journal.pone.0146756.g002.PNG that is referenced in index.html. In at least this instance, the issue to seems to be the case of the file extension. The file contains the line:
<p><img src="images/journal.pone.0146756.g002.png" style="display: block; margin: auto;" /></p>
Note that the file extension is lower case. When I cloned your repository to my Ubuntu machine, I was able to get that particular file to display by changing the file extension to upper case:
<p><img src="images/journal.pone.0146756.g002.PNG" style="display: block; margin: auto;" /></p>