What is this 'border' on the instance icon and how do I get rid of it?

It is making these particular frames behave differently from the rest.

Also please update the View layers and pages in the left sidebar page. Many new symbols have been added and not everyone can keep up with them.

In your autolayout frame (col 1) you have the first 3 Cell layers in Absolute Position. You can turn it on/off in the design panel, to the right of the Y value. It looks like a + sign with the “borders” you’re referring to.