Okay, so the actual problem is the license error from the Get Network EIDs tool. The other error is expected since you didn't finish Get Network EIDs successfully.
The Get Network EIDs tool is a python script tool which in turn launches an ArcObjects executable which queries the network dataset and logs some IDs in a database. The ArcObjects executable is necessary because the network dataset query is available in ArcObjects but not in python. The problem you're seeing is when that ArcObjects executable gets run. For some reason, the executable is not able to check out the Network Analyst license even though you have it.
Other people have reported a similar error message to me, but I haven't successfully determined the cause for any of them, and there's very little that I can do as a developer. Esri Support can't help you with specific questions about the Add GTFS to a Network Dataset toolbox. However, for the other users with this problem, we were able to reproduce it with a simple ArcObjects executable that does nothing except check out an ArcMap, Engine, or Server license (depending on the product installed) and then a Network Analyst license. It will print out something to the console indicating whether it succeeded or failed. Since that is a generic problem, Esri Support (or Support at the distributor for your country) should be able to help you figure it out.
Here's what to do:
- Download and extract this simple ArcObjects executable and put it somewhere on your machine (preferably not on the Desktop): SimpleNALicenseCheckout.zip - Box
- Open a command window
- Run the executable. You will probably see it fail with the same error as the Get Network EIDs tool.
- Call Esri Support, show them this GeoNet thread and the simple executable, and see if they can help.
