I'm not familiar with that particular Fluke meter, but I did take a quick look at an online manual. Based on your response, it appears you correctly placed just ONE wire inside the sensor zone. If the pump was energized, then you should have received a valid reading. But again, 0.1 amps can not be accurate if the pump was energized and pumping water.
If I were you, I would conduct a simple test to verify your meter is reading amps correctly. (unless you have a trouble light or lamp with the bare wires exposed, you may have to make yourself a short extension cord with exposed wiring to conduct the following test) With a 100 watt light bulb energized, place either the black OR white wire inside the sensor zone. With the meter selector set to <A> you should get a reading of approximately 0.8 amps. If so, then your meter is reading correctly.
However, I still say that the pump is pulling more amperage than you've indicated if it is truly energized!