Set 1 (@data):
g123|10249875
g948|32004040

Set 2 (@ref):
g123:1|10249870
g123:2|10249875
g123:3|10249871
g984:2|94950595
g984:1|32004040

##</code><code>##

foreach $elem(@data){
   ($sub,$max)=split/\|/,$elem;
   @found=grep /^$sub:/,@ref;
   foreach $f(@found){
      ($id,$time)=split/\|/,$f;
      if($time ne $max){
         push @set,$id;
      }
   }
}

##</code><code>##

@set:
g123:1
g123:3
g984:2