While there are reasons why aliens could look like us (anything is possible), there are far more reasons why they would not look like us.

Why Not?

When we are talking about the biology of different species, even species with no common ancestry at all, there are universal traits - meaning that there are problems that all species will face with a common solution, e.g. the Square-Cube law means that larger alien species will have thicker-looking limbs and a heavier skeleton than smaller ones.

There are also parochial traits - meaning that while there may be a common problem, the approach to solving it can vary, e.g. many terrestrial species have eyes, but insects have compound eyes, while vertebrates have eyes with a retina and lens.

Given that the majority of features of an alien will be parochial traits, the odds of an alien with no common ancestry looking human is quite low.

However, there are a number of reasons why a sentient alien would have similar traits. A sentient tool-using species must have a brain (or brains) big enough to do the processing necessary to support sentience (a universal), but they need not be in a head (parochial). A tool-using species must have appendages able to manipulate the objects that they use (universal), but they need not look like human hands (a parochial). They need not be mobile, though they probably would be, and they need not be warm-blooded, though there is a fair chance that they would be.

So, we have a mobile, tool-using alien. This means it must have some means of being mobile, but this could be almost anything, a slug-like foot, hundreds of cilia, wings - or legs, amongst even more possibilities. If it had legs, there could be as few as one, or there could be more. The odds of there being two is fairly low, as it is not the most stable configuration.

Our tool-using alien must have some way of manipulating the environment, but evolution (which is probably another universal) need not adapt a locomotory appendage to that task - what if an alien's manipulator evolved from, say, it's tongue? Elephants' manipulators evolved from their noses/lips after all.

As for aliens being fleshy, that again is a parochial solution. Depending on the gravity levels in the alien's place of origin, they may be incredibly fragile with soft, easily torn flesh to incredibly tough with flesh that is more like wood. There are ways that beings with a body structure composed almost entirely of woody material could move, for example by expanding and contracting cells asymmetrically within an appendage. Plants move (usually very slowly) this way.

Why

However, if we have an alien species that does have human-like traits or is even "mostly" human, how could this occur?

One logical explanation is that some other species (that probably doesn't look human) has been abducting humans (possibly for millennia), relocating them onto other worlds, and modifying them to fit their new environment and/or to meet whatever other requirements they may have had. It would probably become evident that there had been interference if said world was examined thoroughly by scientists.

If there is just one species out of many (aside from humans) in a setting that looks humanoid, this would also be reasonably plausible.

However, to have a setting where almost all the aliens are humanoid is probably the result of either a limited imagination on the part of the author, or is a calculated strategy - the author may want to make a social commentary that would offend a real-world group, but by saying that "aliens" are doing it, the commentary becomes socially acceptable. The setting may have been designed for visual media such as a movie or television, and aside from reasons of budget and practicality, audiences relate better to more human-like characters. There is also the factor that if a story contains very alien aliens, it is more difficult to keep the story about what the aliens are doing rather than what they are.