There are many things you could be encountering, since you didn't post any code we will have to consult the oracle to determine what the nature of your problem is:

The oracle says: "Lightning strikes."

# store the array in a variable
my @foo = builder();

# pass it to another function to print the contents
printer(@foo);

# build array of arrays (sic) and return it
sub builder {
    my @built = (
        [qw/a b c d e f g/],
        [qw/1 2 3 4 5 6 7/],
    );
    return @built;
}

# print the data
sub printer {
    my @array = @_;
    foreach(@array) {
        print join(' ',@{$_})."\n";
    }
}
__DATA__
a b c d e f g
1 2 3 4 5 6 7
[download]

In the interest of TMTOWTDI and as a newbie as well, I also like this approach for displaying without the join:

# print the data
sub printer {
    my @array = @_;
    foreach(@array) {
        print "@{$_}\n";
    }
}
[download]

use strict;

my $AofA = buildAofA();

display_AofA($AofA);

sub buildAofA {
   my $AofA = [
       [qw( one two three four )],
       [qw( five six seven eight )],
       [qw( nine ten eleven )],
   ];
   return $AofA;
}

sub display_AofA {
   my $AofA = shift;
   foreach my $array (@$AofA) {
      print join(',',@$array), "\n";
   }  
}
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        open FILE, "<input.txt";
    open OUTP, ">output.txt";
    undef (@matrix);
    while (<FILE>){
    push @matrix, [split];
    }
    &dataconvert; # this is where it branched off to 
                  #change up the data
    select OUTP;
        for $i (0.. ($#matrix)){
    print "@{$matrix[$i]} \n";
    }
[download]