This affect is not limited to loading the same module twice, as it will happen if you load two modules that export subroutines of the same name (in this example 'foo').

I presume this is a warning to prevent incompatible modules being used at the same time?

For example

one.pm

#!/usr/bin/perl -w
use strict;
package one;
require Exporter;
our @ISA = ("Exporter");
our @EXPORT = qw(foo);
sub foo {
    print "how do you do\n";
}
[download]

two.pm

#!/usr/bin/perl -w
use strict;
package two;
require Exporter;
our @ISA = ("Exporter");
our @EXPORT = qw(foo);
sub foo {
    print "Salut toi! Ca va?\n";
}
[download]

trial.pl

#!/usr/bin/perl -w
use strict;
use one;
use two;
foo();
[download]

result of running trial.pl

[~/] perl trial.pl 
Subroutine main::foo redefined at /usr/local/lib/perl5/5.8.2/Exporter.
+pm line 60.
 at trial.pl line 4
Salut toi! Ca va?
[download]

Note, if you switch the use statements, main::foo points to one::foo instead of two::foo

modified trial.pl

#!/usr/bin/perl -w
use strict;
use two;
use one;
foo();
[download]

result of running modified trial.pl

[~/] perl trial.pl
Subroutine main::foo redefined at /usr/local/lib/perl5/5.8.2/Exporter.
+pm line 60.
 at trial.pl line 4
how do you do
[download]