A recent episode of "Revolution" covered one of my fears: being tricked into solving a code problem through a dream.
After I watched "Inception" it was clear to me that the real value wouldn't be tricking an executive into revealing some small memorized thing, or even introducing an idea. No way! A skilled consultant costs hundreds of dollars an hour. Because time is accelerated in the dream, you could get days of work out of a consultant, overnight. Ideally there would be a friendly agreement between the consultant and the business, and there would be a light workload and luxurious benefits at no cost. But I could easily see it turning into a sweatshop condition, or an intense training simulation, or like in Revolution/Inception the dream challenge could be dumped on you.
So that's one of my metaphysical fears. Here are some more equally illogical, but nasty ones:
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slipping into an alternative universe where programming is completely different. JavaScript became the language of the web through a complex series of agreements and happenstance. Tweak a few things, and I won't know how to do my job. I can transition between languages, so I could pick it up, but the first day would be a bad one.
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time warp. Despite plenty of fiction on it ("Groundhog Day" being genre-defining, "12:01" being particularly haunting) no one has real-world experience with time warps. So if I were in a time warp, I'd have no hints to determine how I entered or how I would exit the time warp. I thought about this often in the subway tunnel between SF and Oakland, where there are no references and it'd take a lot of time to recognize a loop.
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consciousness being simpler and more emergent than expected, so laptops or supercomputers gain sentinence before we have a real plan for it. Huge blow to humanity.
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solipsism. If tremendously unlikely things happen to me, then there could be issues with reality itself. I guess it would be worse if someone else had the solipsist powers, like in Haruhi Suzumiya.
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dissolution of scientific laws. Things are no longer repeatable or deterministic. Atoms could stop working. Bummer.