All changes are committed instead individually selected lines

Problem

1. Changelists are enabled in Settings | Version Control | Changelists
2. A non-modal commit interface is enabled in Settings | Version Control | Commit
3. Select specific lines to be committed
4. All the lines are committed instead of specific ones.

Cause

Pre-commit hooks which contain git add in the script.

Resolution

Modify the pre-commit script or disable it completely as shown on image: