This is a common issue. What you did was you uploaded the main folder of the plugin instead of the sub folder.
Plugin folders have a main and a sub folder.
main/sub/files you uploaded main/sub/file
you should have uploaded sub/files
so go into your ftp now and remove all of those and then upload the sub folder and you will see them.
Example: if i had a plugin named myplugin it would be stored in myplugin/myplugin/(all my files)
so when you upload just upload myplugin/(all my files) instead of myplugin/myplugin/(all my files)
Let us know if you need more assistance.