Others have given more advanced solutions to your issue.

The main issues with your code were:

• The expression <end/> is a FILE GLOB. Please look that up since this was obviously unintentional
• The expression was incorrect in another sense: the data has "/end" with the slash before "end"
• The logic to collect information was incorrect, and
• @values was wrongly scoped

With these corrected, the following modification to your code provides the expected answer:

use strict;

#open(IN, '<', "test.in") || die "\nCan't open test.in\n $!\n";
my @values;
while(<DATA>) {
    if(/<ref id="(.*?)">/){
           push @values ,$1;
           next;
    }
    if(m|</end>|){
        print "New Group: @values \n";
        @values=(); # Empty it
    }
}
#close(IN);
__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>
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