I've recently bought Nexus 5x from amazon and it came with android 7.0.0, but official specification says that it comes with android 6. So question: does it mean something wrong with my device (used, refurbished etc)?
It's most definitely refurbished. Android 7 doesn't come preinstalled on the Nexus 5X brand new.
There are several ways for testing whether an Android phone is refurbished. How to tell if your phone is refurbished gives a list that you can try, to begin with. It is not guaranteed to work, but it is worth trying.