Yes, if you read in many different files, perform the same types of operations on them, but don't create a function to handle those manipulations. Or at least a loop. People who do this tend not to be diligent about error handling and tie themselves up in global variable failure knots.

# don't do this
my @lines;
open(DATA, ">file1");
while (<DATA>) {
    push @lines, $_;
}
process(@lines);

open(DATA, ">file2");
@lines = <DATA>
while (<DATA>) {
    push @lines, $_;
}
process(@lines);
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No, if you have a couple of functions that do different things but use lexical variables within the functions.

sub read_file {
    my $filename = shift;
    open (DATA, ">$filename") or return;    # could die on error
    my @lines = <DATA>;
    return process(@lines);
}
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The use of different variables for different things is preferred as when someone reads/debugs your code it is clear that the different instances relate to different data.
All compilers nowadays (including perl, according to the excellent explenation here) define the scope of the variable, so the "dangling" variables get cleared away as soon as they are done.

An exception for this is objects that require expensive setup (like ftp connection for example). In these cases it makes more sense, from optimization point of view, to reuse these resources.

Sorry for not giving actual timing data, maybe someone will benchmark it.

Here is a benchmark:

#!/usr/bin/perl -w

use strict;
use Benchmark;

timethese(1000, {
    'global' => '&global',
    'local' => '&local' });


sub global {
    my %hash;
    for(1..100) {
        for(1..10) { $hash{rand(100)} = 123; };
    }
        %hash=();
}

sub local {
    for(1..100) {
        my %hash;
        for(1..10) { $hash{rand(100)} = 123; };
    }
}
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And it gives:

Benchmark: timing 1000 iterations of global, local...
    global: 14 wallclock secs (13.47 usr +  0.01 sys = 13.48 CPU)
     local: 14 wallclock secs (13.33 usr +  0.02 sys = 13.35 CPU)
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so it seems like there is not much difference.