When the N6 first came out and people started tinkering, it was quickly found that changing display density settings in the build.prop would/could cause this. I have factory DPI set, and I have run in to this once since November, and it was also with YouTube now that I think about it...
If you've tweaked your DPI, I would suggest trying to go back to stock and see if the problem resolves. If you haven't modded the DPI and it's happening often, perhaps try a factory reset.