For a start

while (@thisfile) {
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doesn't do what you think. In particular, it is not

for (@thisfile) {
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Next:

$seen{b} <=> $seen{a}
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compares the values for keys 'a' and 'b', not for the two sort variables' ($a and $b) contents as you are hoping. Cleaning those problems up, fixing a few other style issues and providing some sample data gives:

use strict;
use warnings;

my $fileData = <<DATA;
Greetings,
I've been trying to put a word frequency counter together but I keep g
+etting an
unitialised value in pattern match. I'd be grateful if somebody could 
+let me
know what I'm dong wrong.
I added a line to get some repeated words.
DATA

my %seen;

open my $inFile, '<', \$fileData;
for (grep {chomp; length} <$inFile>) {
    $seen{lc $1}++ while /(\w['\w-]*)/g;
}
close ($inFile);

printf "%5d %s\n", $seen{$_}, $_ for sort { $seen{$b} <=> $seen{$a} } 
+keys %seen;
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Prints:

    2 a
    2 to
    2 i
    1 i've
    1 know
    1 put
    1 if
    1 unitialised
    1 greetings
    1 i'd
    1 frequency
    1 wrong
    1 let
    1 could
    1 in
    1 keep
    1 line
    1 repeated
    1 trying
    1 what
    1 value
    1 me
    1 match
    1 grateful
    1 i'm
    1 word
    1 be
    1 some
    1 somebody
    1 but
    1 added
    1 words
    1 dong
    1 been
    1 get
    1 together
    1 getting
    1 pattern
    1 counter
    1 an
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