This is a ridiculous question and please don't be insulted, but I'm just wondering something.
When you're placing the squares on the rectangle, are you lining them up as indicated in the diagram in the pattern?
Or are you stacking the square directly on the rectangle so that 3 sides of the square (top, outer edge and bottom) line up exactly with those of the rectangle?
And once you get it figured out, MadQuilter's #5-6 are really good tips. The all were, but those are especially helpful.