Because some customizations can break Project Web App pages we have always blocked SharePoint Designer from editing/changing a PWA master page - and in the 2007 version I even blogged about it. Time moves on and there are now new ways to play about with master pages, and new ways to break PWA! Design Manager was released a couple of years ago to allow easy branding of SharePoint pages, and this isn't something we can block for PWA so it is possible to break our pages - so for the best experience do not update the master pages on a PWA site.
As with any 'unsupported' change that doesn't always mean you shouldn't do it - but just be prepared that it might break something, so test thoroughly and then if you do find a break you will need to either fix it by reverting or further modification. We can't help you from support to troubleshoot the break - our support only extends to reverting to the original master page.
The most recent issue I've heard of where a master page caused problems affected some of the charts in the Resource Center - but I'm sure there are many different ways that things might break.