You want to sort the words in the regular expression by descending length :) Or alternatively, use \b to match only whole words:
my %trans = (zero => 0,
one => 1,
ones => 11,
two => 2,
three => 3);
my $words_re = join "|", map quotemeta, sort { length($b) <=> length($
+a) } keys %trans;
$string =~ s/\b($words_re)\b/$trans{lc $1}/ig;
Otherwise, it could be that one matches before ones.
Update: choroba spotted that the length($b) and length($a) were missing
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