I simply ignore it. Honestly, if you really need MS fonts, get yourself a copy of a Windows 10 ISO file
WebUp8 has an excellent how-to
It talks about Windoze 8.1 but 10 works as well. I got all Windoze fonts this way. I’m not an avid fan of MS fonts but some programs I use, especially KeePass2, simply has empty squares in the window title. It’s not always the case. I didn’t have this issue with 14.04, but with 16.04 it reappeared.
I use the Java PPA from WebUp8 and maybe next time I don’t select the option to download MS fonts. I wonder if we still have the option.
Again, if you can live with the occasional pop-up window, leave it as is and let it be fixed with an update. I tend to break things when I try to fix them by myself 