A layer in your 3D document has a layer offset applied in its base height property settings.
Solution: During an edit session, the Layer Offset value will be disabled and the features returned to 0. Once you finish your edits, the offset will be reapplied automatically.
More Information: Visual effects, which are often created from cartographic layer offsets, are not supported when editing in 3D. You can access the current base height settings for layers in the Layer Properties dialog box by clicking the Elevation tab in ArcGlobe or the Base Heights tab in ArcScene.