@varunksaini or anyone else, did you find a solution for this? I am having the same issue with ST3 on OS X 10.11 with Python 2.7.
The following prints at the start of every build output from Python and from Ruby (and possibly other build systems):
They appear to be escape characters to move the cursor in the output console. This issue does not occur with ST2 but I rely on some plugins only available to ST3 so I do not wish to change.