OK. I had another look at your program.

I rewrote it and left out all the fancy formatting (which really put me on the wrong track) and brought it down to the bare minimum.

As you will see when you run the program, it works perfectly and the output is as expected:

use Modern::Perl;

my %count;
my $railcarcnt = qr(Boxcar|Reefer|Flatcar|Tankcar|Gondola|Hopper);

while (<DATA>) {
    $count{$1}++ if /($railcarcnt)/i;
}
foreach my $word ( sort keys %count ) {
    say "There are $count{$word} $word Car(s)";
}

__DATA__
B&LE:65065:Hopper:Home
B&LE:65700:Hopper:Home
VM:51142:Hopper:Home
OS:1400:Hopper:Home
HT&SF:1234:Flatcar:Away
NMBS:999:Reefer:Gone
[download]

Output:

There are 1 Flatcar Car(s)
There are 4 Hopper Car(s)
There are 1 Reefer Car(s)
[download]

I can only guess that there must be a data issue or that the code you posted is not the code that actually ran to get you that output.