I've created a .pcap file using Wireshark. When I attempt to open it in Networkminer, it says it can't open the file because the file is not a .pcap file. I used the standard Wireshark "save as" to save it as a .pcap file from Wireshark. Has anyone else had this issue? Anyone know why this would happen?

I suspect that you're running Wireshark 1.8 or later, which uses the PcapNG format as default. You can convert from PcapNG to PCAP at http://pcapng.com or use editcap.