Now I don’t have an emonpi, so what I am saying might not apply. I have had experience with many power meters and did this professionally during the start of energy deregulation in the US. If any of my meters read negative 40W I would be very concerned.
Here is what I would do.
Remove the CT from the power line so it should be measuring 0 current. It should now show 0 power.
Connect the CT to one circuit, not the whole house, where you can control the loads. Now put know loads that are linear (like old fashioned incandescent lights) and see if they match. This allows you to see how accurate and linear the response is.
Now, it is possible that @Robert.Wall is correct and you should just subtract out 40W in emoncms. But I believe @TrystanLea might be correct. If you have the CT on one phase and the VT on a different one they will be +/-120 degrees or +/-240 degrees off. This will certainly give you the wrong answer and I suppose it could go negative. It would also give you incorrect information about your actual usage. Your graph is interesting, with the regularity of negative to 0 transition. It also doesn’t show just the kettle coming on and off with everything else being constant, so it is not clear how accurately it is being measured. It might be that it is not measuring the kettle correctly. I don’t know much about the power systems in your country, so don’t know how likely your building would be to have 3 phase power coming to it. If you can see the number of wires coming into the service, ie if they are not in conduit, that would be a clue.
Only you can decide how much detail and accuracy you need/want. You are getting a picture of your utilization now, and you can use that to make decisions that will be based on some data. I have some CTs that give me a picture of the power utilization that is pretty good, but I have since learned that they really aren’t that accurate because they have a pretty inconsistent phase error that varies by several degrees so not easy to compensate. Do I spend real money to get a better picture or continue with what I have. It always a choice .