The upgrade guide at http://mantisbt.org/docs/master/en-US/Admin_Guide/html-desktop/#admin.install.upgrade says "You might have to copy as well other custom files such as logo, favicon, css, etc.".
I found it useful if this paragraph would also have a hint that additionally installed plugins have to be copied, too. I only use the "BBCodePlus" plugin and needed a couple of minutes to find out why this does not work anymore after upgrading my MantisBT installation. Just copying the folder did the trick, and I would have done it if it was outlined in the documentation. :-)