Ok, What I mean is that your plugin uploads the files at “wp-content/uploads” in a wordpress single and multisite installation.
In a wordpress single installation this is correct.
But in a multisite wordpress, is not correct. Each site must have its files in its directory. For example, blog1 has the files in /wp-content/blogs.dir/1/ and blog2 has its files in /wp/content/blogs.dir/2/
… and the directory wp-content/uploads is not used.