Take the Wrench, shift+right click on an item interface pipe. The pipe is removed as block and drops as item, but the interface gui is opened for the now non existent pipe. Some options in the gui result in various crashes.

I am experiencing this exact thing. Sneak+right-click both opens the item interaction pipe GUI interface AND removes the pipe. Ver: 1.8.9-2.3.5

This was fixed in 2.3.6

I'm using the latest version from Curse. Mind updating that then?

The 2.3.6 version is labeled beta for the time being, the issue you are having is fixed in that version. http://minecraft.curseforge.com/projects/neotech/files/2281972