Why does Epoxy Hardener sometimes change color in the bottle?

Once the hardener bottle has been opened and exposed to oxygen discoloration begins this is called oxidization. Even a little contact with the air over time will cause oxidization to occur. 

Yellowing can still occur even if unopened because the HDPE plastic bottles it comes packaged in does breathe a little.

But no worries, even if the hardener has yellowed it can still be used, and it will cure properly. Once it is equally mixed with resin (which does NOT discolor) the final product will cure crystal clear.