I disagree with just about everything you said being a problem except the process of cleaning up is absolutely required.
Notably feature flags triggering incidents is expected and desired vs the alternative of shipping the code and having to roll a release back because there is no other way to remove the feature from prod.
Notably feature flags triggering incidents is expected and desired vs the alternative of shipping the code and having to roll a release back because there is no other way to remove the feature from prod.