umm interesting, APIPA is link local and shouldn't be communicating besides its local subnet, are you sure that your Ping is going to the server ? Setup a wireshark or tcpdump and see if icmp sourced from your PC is reaching the server on that APIPA configured nic for sure.
Seeing the ARP in the router or switch should be of any concern because a machine generally uses arp to check for duplicate ip addresses even in case of APIPA address configuration.
Manish