Could be that you had some double vertices (maybe from extruding and then using CTRL Z to undo, which undoes the Transform, but not the Extrude). Then the rounded planks would be connected to those double verts, causing the ‘indentation’.
Something like this has happened to me a lot: I followed a tutorial to the letter, but at a certain point, my results were (completely) different! Then, when I couldn’t figure out what I was doing wrong, I just started over and then it worked (usually finding out what I did wrong the first time, by doing it again…)