I was working on the "Landing on the Mun with Extended Stay" contract today. I sent a small lander with a rover that had a command seat to the Mun and visited all the sites with the rover (and a kerbal).
Upon leaving the rover and getting back into the lander I noticed that I lost the contract progress for visiting the sites. Switching back to the rover showed the progress as completed again (but not on the lander I was planning to return with, even though it had the kerbal that visited the sites in it).
Since one of the requirements to complete it is to return home safely, it appears you can only complete it by visiting all sites with exact vessel that you're going to return with (and kerbals alone don't count).
Was just wondering if this is intended or just a limitation in the way contracts are tracked.