Hasn't seriously happened to me yet... I only read one book at a time. However, a few times I've opened up MobiPocket to read something, forgetting that I had recently added a book, or checked a reference in another book, when I closed it. So I'm expecting to read one thing, get about 2 sentences in, and realize: "This is a different story. Whuthehey?"
More often, when I'm writing, I confuse myself with some of the SF terminology I use... because, depending on the book, and the futuristic time period, I may be using different tech or different tech names to mean roughly the same stuff. "Oh, wait... do I call computers in this book 'computers,' 'Intelligence Systems,' 'secretaries,' 'HAL,' 'pocket brains,' or 'iThink'?"