The key issue is your parameter assignment in test_function. @_ is an array list so assignment in a scalar context will get you the length of the array list - in this case 1 because there is a single parameter passed to test_function. The fix is to use a list assignment:

use warnings;
use strict;
use feature qw/say /;

my @test_array = ([1, 2, 3], [4, 5, 6]);

test_function(\@test_array);

sub test_function {
    my ($ref_array) = @_;

    say scalar @$ref_array;
}
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Prints:

2
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Note too that in Perl since last century you don't need to call subs using &. In fact doing so can cause some very nasty to find bugs.

Dumping $ref_array instead of @_ may have helped you pick up the error.

Update: corrected brain fart - thanks haukex