There are a stack of things that look odd in your code with the top of the list being if(<end/>){. However, the following solution to your problem as expressed may help:

use strict;
use warnings;

my $str = <<DATA;
<ref id="ref1">
<ref id="ref2">
<ref id="ref3">
</end>
<ref id="ref4">
<ref id="ref5">
</end>
<ref id="ref6">
<ref id="ref7">
<ref id="ref8">
</end>
DATA

open IN, '<', \$str || die "\nCan't open test.in\n $!\n";

local $/ = '</end>';

while (<IN>) {
    my @avalues = /="([^"]+)"/g;

    next unless @avalues;
    print "New Group: @avalues\n";
}
close (IN);
[download]

Prints:

New Group: ref1 ref2 ref3
New Group: ref4 ref5
New Group: ref6 ref7 ref8
[download]

Note the \$str trick is just to avoid requiring a file external to the sample code.