If a custom entry is made such as ThermalFoundation:Ore#4 for input it will crash the server.
ThermalFoundation:Ore:0#4 works fine. The meta is intended to be included as per the instructions (which I didnt notice until I started digging around the code for the crash issue). A more graceful way of handling the error may be a good enhancement for the mod in the future

What is the crash exactly?

Alright, it was just an out of bounds exception.

With this commit, it'll swallow the crash and print an error to the log:

LogHelper.error("Error adding " + (input ? "inputStack" : "outputStack") + ": " + stackString + ". Is it formatted correctly?");