Command Module bugged?

[doctorsuits]

I'm having a weird issue that I can't seem to find much info on. I've had this happen multiple times now and can't seem to figure out what the issue is.

I'm flying a ship I built with a mk3 Command Module, which I then dock with a mk1 Lander Can (both go up in the same vessel) and take that into orbit of the Mun. Once there I transfer a Kerbal over to the lander, disconnect and then land on the surface of Mun. I do my thing there and then head back into orbit to dock with the CM. On approach I can see the RCS thruster cloud from the CM thrusters, but when I switch to control the CM, the RCS thrusters are not on and turning them on and off again doesn't do anything. After connecting the two craft I transfer my Kerbal back to the CM and make my return to Kerbin. All the while it looks like the CM's thrusters and firing but everything says they are not. Once I make my return and splash down I cannot recover the vessel, nor can I go to the science center or save or anything. I can only reload from my latest save.

When reloading from the "Persistent" save, I reload when the lander is returning to orbit from Mun, but the CM is now nowhere to be seen and the two Kerbals from the CM are in a pop up right when I load in saying they completed their trip.

Any help anyone can give would be greatly appreciated. I would hate to have  this occur every time I go to land on another planet or moon.

[OHara]

If you are using KSP version 1.11.x, this sounds very much like a bug that appeared in version 1.11.0 (link)  Often, when players find a work-around to avoid a bug, we post them on that bug-tracker --- but so far no solutions posted for that bug.   It seems like only a small number have people have noticed it, so hopefully the conditions to hit that bug are rare.

(You might already know, many players move their KSP installation so that the new version goes in a separate directory, avoiding overwriting the version we have been playing. Then when a new version comes out we can try it out, but if there is anything we don't like we can stick with the previous version.)