There is definitely something fishy going on whenever more than one mission are successfully completed in the same sitting. If i was a betting man, i'd bet there's some memory leak that occurs when the mission is 'won' that doesn't seem to happen when it is 'lost'. Here are some symptoms i have seen:
1) Completed the Wellington mission, then had my dropship wiped out by a surprise Harvester. Reload the savefile taken just before landing in Wellington. Now the location of the mission is different. I forget where.
2) I once saw some graphical corruption in the Buy/Sell Equipment screen - there was a white rectangle that covered two names in the equipment list. Sorry, i did not get a screen shot. Anyway it hasn't happened again since, and the only different thing i can think of that happened before this was that i had finished two missions back to back.
I have now begun quitting the game after every mission rather than just reloading. Since i started this, i have not seen any more wierdness