You can bet that the different IDF Bases received orders (months ago or longer) on how to react in conflicts with the Settler Thugs. Probably: "Injuries to attacking settlers and/or Hilltop Youth should be kept to a minimum. Avoid firing of weapons at all costs, do not use standard dispersal means and attempt to use non-lethal means to break up any intrusion attempts." That would be included with a directive to immediately call the base commander, who in turn calls one of his superiors. But in any case, the IDF's failure to respond demonstrates that their reaction was most likely the careful execution of a pre-determined (as roughly outlined above) contingency plan for situations just like this one.
from the article: Dozens of rightists break into IDF base in West Bank, wound officer