I’ve been having the following problem since I started using Sublime Merge (about 10 months ago or so), it’s hard to explain so I’ve recorded a video:
When staging a hunk, this unrelated junk change that appears is always near the end of the file.
Discarding error that I’ve showed in the video wasn’t caused by previous staging, it’d happen anyway.
At the end of the video is my .gitconfig setting. From the debug information regarding the file in the video, the section “=== Our Modified Files Newline Normalisation and EOL Information ===” says “input - native”.