This looks like a bit of rounding issue. The graph uses the Connect Area Graph (Closest Border Points) node inside one of the sub graphs. It tries to connect areas by matching up the border points that are closest to each other. In this case there are two valid options, because they're square. It picks the upper option. Then the Draw Connections node draws the connection. If it's two pixels thick, it draws one line between the two connected points and one above that. Creating the result you're seeing. If you're using an odd number for width and height, it will always prefer the more centered point, because the Connect Area Graph (Closest Border Points) node prefers points closest to the area centers, which is why this issue doesn't occur in that situation. To solve this, I'm thinking that if there are two equally valid options for connecting two areas, it should pick the bottom one instead of the top one, due to the way drawing works that would make more sense. Sorry if this is a bit of complicated rant. The tldr is that I think I should make a bit of an adjustment to how the node decides which points to connect, so that the connections line up better in a case like this. I'll start working on this soon and I'll get back to you when I've implemented a solution.