What could this signal be?
Your raspberry is a complex device with varying power consumption – that isn't surprising at all, it's a fully-fledged computer with loads of different operational states, its own cascade of power supplies that derive the voltages needed from the 5V input, and the option to connect external hardware.

In any case, you will always see fluctuations in current going into your pi, and thus, fluctuation in voltage drop across your shunt resistor. A computer is not a constant resistance!