Dear Maik,
I assume, that you haven't assigned pumping rates to your well boundary conditions, is that right ?
If you have used multi layer wells, in my experience your boundary nodes work like a vertical connection between all layers, where your well nodes are defined.
A groundwater exchange between all layers is enabled. If you have a layered aquifer with different conductivities, this effect may produce your water level changes.
Best Regards, Henilein