First, bees have an extended visual spectrum that allows them to actually see UV light. We've named this color "bee purple," and plants have evolved together with the bees to take advantage of another visual cue they can use to attract pollinators. In the picture of a cucumber flower below, the left image is what we see, and the right image is a false-color composite of approximately what the bee sees.
So why was he de-powered when dragged into a ship with Kryptonian atmosphere? Why did Zod become overwhelmed with all of these super-senses only when his breather helmet broke and he was exposed to Earth's atmosphere? This can also be explained through the science behind satellites! Satellites are limited to using wavelengths of light that can easily penetrated the planet's atmosphere, especially since the signal has to travel through this boundary twice: first to reach the Earth's surface, then to bounce up to the satellite. Here's a diagram of what parts of the spectrum are the most absorbed by the atmosphere:
What I really enjoyed about the movie was Clark's struggles as a child to understand and control these enhanced senses. He has the equipment to see any wavelength of light, but he doesn't know how to focus it on just one part of the spectrum. Hence his vision becomes muddled with overlapping images of his skin, his bones, and his thermal signature all at once. It's an overwhelming experience for any kid!
My only scientific qualm with the vision examples used in the movie is the trick he did of reading someone's ID badge through a one-way mirror AND through his pocket. Seeing people on the other side of the mirror would have been easy with IR or X-rays, but unless the name on the badge is written with a radioactive tracer or something special, there's no way Clark should have been able to read it. The letters are only distinguishable with visible light, and those wavelengths simply will not propagate through cloth or mirrors. Nice try, alien.