• $last_stop gives an undefined warning.
• $last_stop can be replaced with $Z[-1][1].
• chomp is redundant.
• The if is fine as it is, but the common $Z[-1][1] = $token[2] can be factored out.

my @Z;
while (<DATA>) {
    my @token = split ' ';
    if ( $token[0] eq 'Z' ) {
        push @Z, [ $token[1] ]
           if !$Z[-1] || $token[1] != $Z[-1][1] + 1;
        $Z[-1][1] = $token[2];
    }
}
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