Not knowing Text::CSV_XS other than browsing the perldoc real quick, I can mainly only comment on your code. The main thing I see is mixing lists and ARRAYrefs, and lots of expensive copying back and forth between the two. Here's the first problem:

    # Create ARRAYref to list of 7 elements, with first element "",
    # remaining 6 elements copied from @fields.
    $file2{$id}=["",@fields];
    $file3{$id}=["",@fields];
...
    # trying to access 6th element of $file2{$id} as a list, but it's
    # an ARRAYref to a list with 7 elements...
    my @fields2=$file2{$id}[5];
    my @fields3=$file3{$id}[5];
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You are constructing $file2{$id} as an ARRAYref with [] (correctly). But you're not dereferencing it on access. Why add the "" at the beginning of the list? You're probably looking for something more like:

    # just hang onto the ARRAYref returned from $csv->getline(),
    # unless it doesn't want us to.
    $file2{$id}=$row; 
    $file3{$id}=$row;
...
    # You really did want the 6th column, right?
    my $fields2=$file2{$id}->[5];
    my $fields3=$file3{$id}->[5];
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Next, this is likely not what you expect:

    # Create list with one element as a string concat looking like
    # "ARRAY(0x141ecf8)\tARRAY(0x141edd0)\tARRAY(0x141ee48)"
    my @printline= ( $fields_ref."\t".\@fields2."\t".\@fields3;
    $csv->print ($FILE4,\@printline);
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You've got a string consisting of three ARRAYrefs joined by tabs. So that does match the errors you're seeing. It's probably looking for something simpler, a single reference to a list with all the data in it. Probably looking for something more like:

    # List with 8 elements
    my @printline= ( @fields, $file2{$id}->[5], $file3{$id}->[5] );
    $csv->print ($FILE4,\@printline);
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Last, you need more error checking imo.

Ultimately, I would recommend taking it a step further and just use references throughout, rather than copying lists to refs and back. It's just not necessary, and it causes your syntax to have to switch back and forth as well. References will keep your syntax consistent. There are lots of other ways to optimize this pretty significantly, but I'll leave that to you.