In dev build 2.1.0.0-102, MechJeb consistently fails to decelerate early enough during the final descent stage while using landing autopilot, usually not even throttling up before crashing violently into the ground. I tried this using the MJ pod by itself from a circular orbit 100 km over Kerbin. Similar results for Mun, Minmus, Duna, Pol and probably others. This issue isn't present in the stable release of 2.1.

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in years, have been fixed for years, do not include adequate replication steps, refer to old problems which are no longer applicable, or are difficult to determine what the problem is.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.