I had this error running cowpatty on my machine:
End of pcap capture file, incomplete four-way handshake exchange. Try using a different capture.
Showing this error, I checked the pcap file in kali linux and cowpatty installed in there checked the file as correct.
So I then call google for help and found very useful article. Here’s what you should do:
Get the source first, uncompress, then cd to its directory.
tar xvzf cowpatty-4.6.tgz
Then get the patch and patch cowpatty.
patch < cowpatty-4.6-fixup14.patch
sudo make install