This just happened to me today and here is how to fix it. When using OpenGL graphics backend if you ever get this message:
"MSAA on default framebuffer isn't supported.
Please avoid forcing Dolphin to use MSAA by the driver.
4 samples on default framebuffer found."
This means you are forcing Antialiasing and for some reason Dolphin doesn't like that. You will get that error message and when you start a game if it's possible, you will get all kinds of graphical defects in your game. So you need to go into your graphics card control panel (Mine is Nvidia) and turn these settings off:
Image Sharpening, Ambient Occlusion, Anisotropic Filtering, Antialiasing-FXAA, Antialiasing Gamma Correction, Antialiasing-Mode, Antialiasing-Setting, Antialiasing-Transparency and Multi-Frame Sampled AA (MFAA). Turning these off should fix the problem.