There is no problem and what you see is intentional behavior. Assuming that you have build catkin_ws2 without catkin_ws1 being source before.
See https://answers.ros.org/question/64702/overlaying-multiple-catkin-devel-spaces-at-the-same-time/ for a similar question which describes a workaround (sourcing the second workspace with the option --extend) but also mentioning the potential pitfalls.