I'm currently building a very large model, and over the course of the build, especially early on, I kept accidentally adding 1x2, 1x4, and 1x6 bricks without pin holes. These pieces definitely are going to mess things up when trying to Bricklink the parts, and pretty much all of them are going to require some disassembly to swap out manually. I ended up with over 80 of the suckers in my model. My suggestion is mainly to move these pieces in the part selection menu, so they aren't right next to the proper bricks with pins. Either at the end of the Brick section or even just a few spaces away would make things a lot easier. Side suggestion, make a button that swaps one piece for another, but I know that's a bit more far fetched.