The general issue is that when an mtu mismatch on interfaces occur all kinds of strange and unpredictable packet loss and error can occur. So using Jumbo frames literally everywhere is fine, no errors.
But at some point you connect to the rest of the world and this transition area needs to be setup carefully so none of the links will have errors.
Most places I've worked and people I've worked with only enable jumbo frames on necessary links and with care end to end to avoid issues.
For devices themselves, they only generate the max size frame that they are aware of. So if the OS and applications are all setup to standard frames they will never use the jumbo payload but their packets will transit the larger mtu size normally.