My 3D layers seems to be having an issue. Geometry Options will not disappear in 3D classic, they are graying out. Also I am losing control of the effects on that layer.
Effects on 3D layers are disabled if you use the C4D rendering engine. You cannot move or rotate any layer with Puppet Pin applied unless you pre-compose the layer before moving, scaling, or rotating it.
I don't know how long Geometry Options popped up on 3D layers with the Classic rendering option open, but it is there on all four versions of AE I have installed on my main computer.
Removing the Puppet Effect removed the bug. Puppet had basically just stopped rendering.