We haven't seen any quirks with the CSS minification, but what you could do is use the HeadHTML webpart and add styles separate from the CSS resource that's being minified. Those separate styles won't be minified.
However, with flex
your best bet is to use the longhand declaration (details on MDN). IE 10 and 11 have a bug that chokes on the shorthand flex
-- which MS has acknowledged.
Hope that helps!