To reproduce this problem:
Create a new repository
Create the following two files "index.php" and "subdir/index.php" directly in the repository directory (where the .hg directory resides)
Right click on the "index.php" in the root directory and select "Ignore Selected Files".
Now //both// index.php files are ignored. This happens because MacHg simply adds the line "index.php" to the ".hgignore" file. However this line makes Mercurial ignore //all// index.php files - and not only the one in the root directory.
To solve this problem one need to edit the .hgignore file manually (and need to use the regexp syntax, as the glob syntax doesn't work). However, MacHg seems to be assuming the glob syntax in the .hgignore file which might lead to unexpected results due to the syntax change.