> I want to know, how to filter packet header duplication.
Really you don’t And that’s why.
> Packets may travel in sequentially over the internet.
Yes for TCP packets.
> If the headers duplicate, the traffic will delay.
NO. The packet never duplicates in-transit. Everything is opposite: when packet is _dropped_ in-transit (or it takes too long to go there and here) only then it duplicates! If you will filter this duplicate packet, it will never reach the destination (or the answer that it is correctly delivered will never reach you)! That’s the core of TCP algorithm and if you change it your traffic will stop completely. I don’t recommend to filter duplicates (you may tune TCP stack instead, to wait for longer delay before resending or to send smaller segments…)
If you still like to filter despite of the danger, go to http://netfilter.org and look for more info. But first, learn more about TCP protocol.