I tried this out in a workspace and it seemed to work ok:
pen := Pen new.
pen place: 200@200.
pen down.
pen goto: 100@100.
xArray := Array with:300 with: 350 with: 425.
yArray := Array with: 500 with: 450 with: 375.
1 to: 3 do: [ :index | pen goto: (xArray at: index)@(yArray at: index)].
Does the above code work for you?
CHEERS!