Remember that the electron probe is cone shaped.
Stigmators control the shape of the cross-section.
When the stigmators are aligned, the probe has a circular cross-section regardless of focus.
If the stigmators are misaligned:
The probe has an elliptical cross-section when out of focus, or
An oversized cross-section when in focus.
This cross-section makes features appear:
Stretched when out of focus, or
Blurry when focused.
X and Y stigmator knobs change the strength of a set of magnets to control probe shape.