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I'm probably missing something obvious, but I don't actually know how to spot the Ninjas and what you're supposed to do in the 4th level Lab to avoid having to fight constantly. No doubt when I realize what it is I'll feel silly, but...

For the ninja ambushes, there's a semi-transparent piece of rope on the ground that triggers it when you step on it. It's hard to see in the tunnel but once you get inside, it's a lot easier to spot.