There are many reasons why an organism might have a trait that does not appear to be beneficial.

1. The trait is actually advantageous even if it does not appear to be.

2. The trait is a byproduct of another trait, which is beneficial. Not all traits are the product of direct selection; traits that are byproducts of other traits are known as "[spandrels][1]", a trait coined by [Stephen J. Gould and Richard Lewontin][2]

3. The trait was fixed by some process other than natural selection, such as genetic drift. Genetic drift can fix traits that are neutral or even evolutionarily disadvantageous.


  [1]: https://en.wikipedia.org/wiki/Spandrel_(biology)
  [2]: http://faculty.washington.edu/lynnhank/GouldLewontin.pdf