ST3 b3092, OS X.
This has to deal with ST automatically saving files before running/building them. ST appears to run the already saved version of code for a brief moment then save the latest code and run it again.
Got a partially copied file after running a Python script even though there was no copy making line in the latest version of the unsaved code before run/build, only in the previously saved file. As if the already saved code started to run, then was interrupted, and the new code was run. The new code ran as expected though.