If that obvious incorrect way happens to match what you're thinking of doing, then that kind of why-not documentation will help.
Warning future developers not to make certain changes is indeed something that should go in a comment. We can make a short comment like, /* if you think you can rewrite this in a simpler way, read commit df037acb first */
There are unfortunate situations when things have to be changed in multiple places together; you must not forget all of them. That deserves comments.
If you have an enumeration that has to pack into 3 bits, there should be a comment warning not to add more elements than eight without increasing the number of bits; especially if there is no compile time assertion for it.