Wrong reason. i don't know what you got when you tried your one liner, but you should have seen something like this:

foo
foo
bar
foo
bar
baz
...
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(because of the randomness of the hash not exactly in this sequence)

Reason is that your small for-loop is inside the while-loop created by -e.

To rectify this you could replace the inner loop with an 'if':

perl -nle '/(\w*)/; print if (not exists $i{$1}); $i{$1}++;' words.txt
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If you really need to do the printing after the loop, you could use END (the seldom used opposite of BEGIN):

perl -nle '/(\w*)/;$i{$1}++; END{print for keys %i;} ' words.txt
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