Comment by GGFPC for You are reading raw packet data through the use of Pcap4J, but are not writing PCAP format files. You simply dump the raw packet data into a file. You need to add the file format structures are well.

Okay I managed to overcome the error by writing to the PcapDumper only the exact number of bytes that were read. But now everything shows as Ethernet on Wireshark. How does libpcap decode the protocol when capturing?