With recent changes to the closing system, there is also a new interface for moderators to change and create site-specific close reasons. This is generally great, since it allows us to set different texts for the flag/vote-to-close dialogue, for the questions author, and for experienced users. However, there is some confusing parts about it too.
Since changing close reasons requires two moderators, it is not so easy to repair mistakes here and therefore it is important that things are clear from the start.
This question is for collecting these issues. To keep things structured, please post one answer per issue.