I will be adding to this OP as I discover new bugs but here is what I have experienced so far:
1- Saves are very odd. Whenever I make a save and try to load that save, sometimes it starts an old save but if I go back to the Space Center and try to load my save from there, then it will load my correct. And sometimes when I load a save it sends me back to the Space Center, but not in the correct save, but from there again I can load the save again and it will be correct.
2- Air Controls get corrupted after a 10 minute plus Surface flight. The trim settings no longer function correctly and my left roll no longer works, even when I pick advanced flight. I have to do a complete barrel roll to orientate myself horizontally again. The work around here is to reload the game.
3- The "B" button does not work on long space flights after a while. And I have noticed that it happens more often if I heavily use the "B" button to select modules. The work around is that I have to reload the game at a save point. And even when I do, then on that particular mission the "B" button not working occurs more frequently.
4- If I have too many saves then I can no longer save my current progress, and also I can not select recover vessel or go back to the space center. Work around here is to delete saves. It happens when I have about 12 saves or more in my inventory load page.
If you guys have found something else please post it. KSP is an amazing game......Lets fix it as a community!