EDIT: I figured out the issue and it is in the hands of the Developer team now.
Hello Everyone,
I'm still very new to this program, but I've been playing with it lately trying to figure out how I can best utilize it. The first thing I noticed was that it was not discovering links between my Cisco and Juniper devices, but I realized that was because I did not have LLDP enabled on my Cisco devices. I have since corrected that, and now NTM is discovering the link; however it is giving the wrong Interface Name (number) for the Juniper device. I looked all over the configuration to try and figure out why it is selecting the interface that it is selecting and I can't find anything unique or specific about the particular interface that NTM is saying is connected. Since it is Juniper (which I'm also somewhat new at) I tried two different things; First, I tried setting the port to "disable" which didn't seem to change anything, then I deleted the port and that fixed it, but that doesn't really fix the underlying issue or tell me why it is telling me the wrong interface name or why it is choosing a seemingly arbitrary interface.
I'm now playing with different stp protocols on the juniper hoping that will maybe change something, but so far no luck. Any help would be greatly appreciated, thanks!
ANSWER:
I don't know why or how, but NTM is mixing up the "Interface Index" number and "Port" number. In the scan that this issue was happening in, I was only scanning two devices; A Cisco 2960 and a Juniper EX4300. They were physically connected as such: Juniper ge-0/0/1 to Cisco Gi1/0/1. The NTM scan was telling me that the connection was; Juniper ge-0/0/17 to Cisco Gi1/0/1. I started looking at why NTM was choosing ge-0/0/17. I ran a "Switch Ports Report" on NTM and saw that the "Interface Index" number for ge-0/0/1 was "507". The port number for ge-0/0/17 was also "507". To test my theory, I changed the physical connection from ge-0/0/1 to ge-0/0/3. I did this because the "Interface Index" number for ge-0/0/3 was "512", which was the "Port" number for ge-0/0/22. I theorized that if I connected it on ge-0/0/3 that the NTM scan would then tell me that the connection was from ge-0/0/22--proving that NTM is mixing up the "Interface Index" and "Port" numbers. I was correct, and when I ran the scan after changing the connection, NTM did identify the connection as ge-0/0/22.
I had a ticket open for this issue and have updated it with this information so hopefully the devs will figure out why it is doing it and fix it.