I´m using this setup for a graph:

box A, is a container.
box B, is contained in box A.

boxes 1, 2, 3, are each starting points of an arrow ending in box B.

boxes 4, 5, are each end points of an arrow starting in box B.

All boxes with an arrow use prebuilt "LeftInRightOut " anchor pattern.

A LayeredLayout object is created and set up to keep anchoring of boxes and horizontal orientation.

Boxes with arrows are setup to my liking, but box A does not move, and box B moves out of box A.

What can I do to fix this behaviour?

Thanks.

Connecting arrows to the container should work too. You could temporarily disconnect the box inside the container, create links to the container, perform the layout and restore the original links.