Apple and Microsoft have both been pushing out updates to deal with various bugs. Make sure you have the latest versions of El Capitan and Office. The Office 2016 upgrade has been one of the rockiest I can recall, it probably didn’t help that it was released almost concurrently with a new version of the Mac OS. Even so, it seems I’ve had more issues with the new MS Office and Yosemite (which is a pretty stable OS now) than I did with the Office 2011 release. Having said that, the printer problems I’ve had with Excel and El Cap don’t exist when I run in Yosemite and even better, Yosemite and Office 2011 get along fine. So does El Capitan and Microsoft’s (limited) online version of Office.
I know there’s not a whole lot of help offered in the above paragraph - we’ll just have to wait for Apple and Microsoft to get their collective acts together and keep downloading updates. In the meantime you might consider using 10.10 and Office or using the online version where possible.