The locations of the chakras are as they are, so they can't be misaligned in a literal sense (I don't think).
So, I'm assuming you mean unbalanced, corrupted, dirty, etc.
The chakras become like this because of karma, which is like cause and effect. Throughout your life/lives and your ancestors, you accumulate the spiritual, mental, and physical development (or lack of). This is reflected in the chakras.
For example, someone who struggles sexually, in whatever way, has issues with their sacral chakra. This may have been caused by previous choices in past lives or programming, like Christian education. Or it could be because of events that have hurt you in this life, too. Likewise, someone who enjoys pleasure and sex, and is emotionally stable, likely as good development of the base and sacral chakra.
This is my understanding and it is obviously not exhaustive, as there is so much more to it.
Hope this helps