Ok, in this case, if you are seeing files in wp-includes that shouldn't be there then you should remove them.
To better determine what files should and should not be present you can use this trick in Filezilla:
http://blog.sucuri.net/2012/11/website-malware-removal-ftp-tips-tricks.html
Have a fresh copy of Wordpress on the left and browse your site files on the right and then press Ctrl+O - the green/white files match and the yellow files will be out of place.
As for Wordfence finding .PHP files with strange names, I am not sure if this is something Wordfence does. Random/strange filenames is only a proxy indicator for malware, though, and does not always indicate an infection (take, for instance, cache files which tend to have very random and strange names)