2D features can be extruded into 3D objects of different heights in ArcScene using feature attributes as the extrusion height. When extruding a layer, the features are sometimes extruded too high; disregarding the actual extrusion heights.
A possible cause for this issue is that the extruded layer is in a geographic coordinate system that measures in decimal degrees. ArcScene cannot extrude a layer measured in decimal degrees.
To solve this issue, project the layer into a projected coordinate system. This converts the layer measurement unit to meters or feet. Use the projected layer to get the correct extrusion.