Two thoughts here. First, it looks like you’re reading the elevation at the bottom outside elevation of the structure, which usually isn’t the sump elevation. That would only be the case if the base thickness is 0. But I don’t think that fully describes the difference, because that would mean that the base thickness of the structure in your example is 72cm, which seems pretty large!
Second, it looks like in the image that the structure depth hasn’t been adjusted based on where the pipe is. I think you have to connect the pipe to the structure first for the structure depth to update based on the invert of the lowest pipe. Doing so might force some things to update correctly.