I've had this happen to our X5 multiple times. Usually when it's been sitting a couple days or more.
I would get a misfire code for 2 or 4 cylinders. I pull the plugs, clean and replace... that would usually fix the issue for awhile. Tried switching the coils around to see if it would follow the problem, but it didn't.
I've changed plugs with new and that will make the problem go away for awhile. Cleaning the mass airflow sensor didn't seem to do anything.
Had an aftermarket AFE air cleaner (oiled type) for years and since replaced it with an OEM a few months ago. Problem hasn't come back since then.
If you don't have a fault code reader... you might consider it. This has helped me save a lot of time/money troubleshooting issues and resetting fault codes:
https://www.bavauto.com/sr-300-16