Janky enterprise crap optimized for IE <whatever> is one big example. The other is old Office stuff like Access databases or workflows dependent on conversion of old file formats. (Last year Office 365 ProPlus purged legacy DBase import for a few months)
IE11 support will go away at some point. Many of those apps are now being updated to work on Chrome -- I know of a few large shops that aren't testing IE or Edge anymore for internal apps!
I do agree that they did a heroic effort on making the update process incredibly reliable. Most non-prehistoric applications transition seamlessly.
Note that I personally equate Windows 10 and the subscription "Office 365 ProPlus". The layers of complexity are astounding. I present to you what I call the "Office 365 ProPlus Build Decoder Ring" - https://support.office.com/en-us/article/Version-and-build-n...
Windows 10 itself has about 8-10 releases that an enterprise needs to think about. Transition from release to release has gotchas and additional Windows-Office gotchas. (For example, the way Office authenticates changes in certain builds) (See: https://www.microsoft.com/en-us/itpro/windows-10/release-inf...)