Your problem is either "ignoring newlines" or "not using a decent CSV parser". Take your pick.

For the first, use chomp:

my %fruit;
open my $fh, "<", "fruit.csv") or die;
while (<$fh>) {
    chomp;  # THIS IS IMPORTANT HERE
    my ($fruit_name, $number) = split m/,/ => $_;
    $fruit{$fruit_name} = $number; # puts key-value pair (apples 5) in
+to the hash
    }
close ($fh);

open my $fn, "<", "fruit_names.csv" or die;
while (<$fn>) {
    chomp; # DO NOT FORGET
    my ($thefruitsname) = split m/,/ => $_;
    my $thenumber = $fruit{$thefruitsname} or die;
    ...
    }
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