I had this happen several times yesterday and today. I thought I had done something wrong but I have now used some time to check this out. This has happened on two different wordpress sites, one with 3.5.1 and the other 3.8.1.
When I downloaded a file, additional code was added to the end/bottom of the file. It looks like it is the entire generated source code for the WP-File Manager page that I download from.
I can work around this by copying edited code and pasting it directly in editing area in WP File Manager but this can cause big problems if one isn't aware of this. Hope you can look into this and find a fix for this problem. I really need this plugin because I unfortunately am not allowed direct access to my files.