knitr not aligning figures to center when image is expanded (.pdf document)

My thoughts.

I think, that this problem exists because of "big amount" of whitespace on left and right sides of your picture.

You can trim it manually and add after with knitr::include_graphics or do it with latex straightaway:

Add to your header:

header-includes:
- \usepackage{graphicx}

Add your pic

\includegraphics [trim={5cm 0 5cm 0},clip]{Ml6KL.png} 
#you can also customize your width/height 
#\includegraphics [trim={5cm 0 5cm 0},clip, width = XX, height = XX]{Ml6KL.png} 

An output:

P.S. If you can - try to find better versions of first two logos(or scale < 1). As you can see - the quality leaves much to be desired...