I Just bought an AE project template and found a spooky layer that controls position and scale for all l layers below, since they are not appear to be bound by parentage expression, I truly can't go to sleep until I find what this "haunted" layer is. I've worked with AE for 5 years and this is really strange to me.
This layer has a transform effect only, and I checked all properties and no expression is applied (as shown in the image attached)
This does show a really uncommon approach. That little black-and-white cookie icon on the timeline indicates that your spooky layer is an adjustment layer. The Transform effect on that layer is applied to the composite of all layers beneath it.