Normally WP Plugins have this structure:
plugins/plugin-name1/some.php
plugins/plugin-name2/some.php
plugins/plugin-name3/some.php
However MU-plugins should have this structure
mu-plugins/plugin-name1.php
mu-plugins/plugin-name2.php
mu-plugins/plugin-name3.php
This is an issue when using composer, as composer is only capable of using (sub) folders. When set to mainlevel folders, composer will delete its contents for each new plugin, resulting in only the last plugin ( in this example plugin-name3 ) "standing"..