We have decended from mammals. But aliens might come from reptiles, or birds, or huge insects. For example, crocodile society is pretty organised and, given a few million years without human intervention, perhaps they’d rule the planet. Or maybe dolphins could do that. I know it sounds silly, because they live in water, but who’s to say that this other planet has any land at all? And as for their spaceships, going from land into the air and then outer space is no easier (or harder) than going from water into air and outer space.
Also, their planet could be much smaller, and everything would then be on a different scale. They could live on a tiny rock with no water, and feed on coal or molten lava. They could even be made of silicon, rather than carbon. Or they could be insects with tiny little spaceships, the size of a human thumb. On a galactic scale, a spaceship 1 inch tall is not much different than a mile-long rocket. Plus insects have more hands to work with, and are better organised than us. All they lack is a brain (and who’s to say they couldn’t develop this on a distant planet, given enough time?).
Their planet probably doesn’t even have any creatures similar to us, and we’d look just as alien to them as they do to us. They probably have no bipeds at all, or even mammals (or else something resembling ourselves would have probably come out of that, as you suggest). But even if they were little green men, or apes for that matter, the evolutionary road would have branched off early enough to make them entirely different (humans had 6 fingers at some point in the distant past, so who’s to say these creatures won’t have scales, tails and antennae?).