__FILE__ is the file name that the __FILE__ token is in, and $0 is a variable containing the name of the program, as given to the shell.
They can most certainly be different - one case that comes to mind is a __FILE__ token in a library called by your program, but there are many others, particularly since you can assign to $0 (with varying effects on different OS), but you can't meaningfully assign to __FILE__.
Example code:
File 1 - firstfile
#!/usr/bin/perl -w
use strict;
print $0 . "\n";
print __FILE__ . "\n";
do 'filetwo';
File 2 - filetwo
#!/usr/bin/perl -w
use strict;
print $0 . "\n";
print __FILE__ . "\n";
It's simplistic, but should show the basic concept.
for(split(" ","tsuJ rehtonA lreP rekcaH")){print reverse . " "}print "\b.\n";
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