If you have two ST3 windows and you run a program in each window then the output for both programs will appear in the build output of the window which was executed first. There was not such a problem in ST2: each window had its own output.
If you have two ST3 windows and you run a program in each window then the output for both programs will appear in the build output of the window which was executed first. There was not such a problem in ST2: each window had its own output.