Why when cloning liquid simulator its output changes ? I’mean both of 'em change path.
What version of Phoenix are you using? Is this Max or Maya?
Latest. max. That behavior is about several months from today. So, literally it is not build number dependent 
Yup, if you clone or instance a simulator, $(scene_path) or $(scene_dir) macros in the simulator’s paths get deconstructed into their building blocks, respectively:
$(dir)\$(scene)_Phoenix_frames\$(nodename)_####.aur
$(dir)\$(scene)_Phoenix2_frames\ND$(handle)_$(nodename)_####.aur
If this did not happen, the copy/instance would be empty without a loaded cache, because $(nodename) is different for the copy, and $(handle) is different too.
Is this a problem for you?
They are both changes. The one that is a source for the copy and the copy itself.
I’m not sure whether it is a problem or not