EGit and Eclipse modifies .gitignore file but it should not
By default, EGit automatically adds resources marked as "Derived" to .gitignore. A typical example is the bin folder in a Java project containing the compiled classes.
You can disable this by going to Window > Preferences > Team > Git > Projects and deselect "Automatically ignore derived resources by adding them to .gitignore".
There was also a bug in EGit where it added entries when the Eclipse model and the filesystem were out-of-sync, see bug 421610 (fixed for EGit 3.5).