Student or Learner
Could this be ambiguous:
"He was shaking with fear."
because definition 6a & 8a of "with" from my dictionary (-- macmillandictionary.com/dictionary/american/with ) apply equally well to the sentence. The shaking could be either accompanied by fear (but not caused by fear), or the shaking coulde be caused by fear.
As a NES, but not an English teacher:
I would normally read it as meaning that fear was the cause of the shaking.