No, seems like now it happens only when I click on nodes in the graph with mouse, but there it is acceptable, understandable — the focus actually was in the graph, so it makes sense to move the focus back there, when one navigates back and forth.
It still allows to move the cursor in the edited note however, even though the focus is in the graph at those moments, which can be a bit confusing, because then OPT ENTER will not navigate to note under cursor, since the focus is in graph.