The rendezvous autopilot is great, but just like everything of mechjeb, has OCD. The rendezvous autopilot tries to get you within 100m, and most of the time tries to get as close to 0m as possible.
This is how I just lost half my space station in orbit around kerbin, because the rendezvous autopilot tries to "park" it inside.
This is actually very dangerous for people with big space stations, as the ship WILL get closer than 50m
I'd like a change which makes it possible for people to set the minimal distance to the target.

"Desired rendezvous distance" would be an excellent option.

Closing this as an old MechJeb issue. Many MechJeb issues have had little interest in years, have been fixed for years, do not include adequate replication steps, refer to old problems which are no longer applicable, or are difficult to determine what the problem is. This issue is being closed for one of those reasons. We apologize for any inconvenience, but keeping the TODO list tidy helps the developers.

If this bug/issue is still a problem, please open a new issue. For bugs please try to include a Minimal, Complete, Verifiable Example that explains all the steps required to replicate the issue. A link to the KSP.log file should be ideally included, but is often not sufficient information. Screenshots or short videos are often the best way to show a bug.