Unit A is the corner that will be half of the 6" finished block. The short sides should measure 3 7/8" and the long side, the bottom edge, should measure 5 3/8", as yours does. Center unit A to unit B and it will be the correct size--the tails that stick out are supposed to stick out.
How did I figure this out? I drew a 3" square on paper, drew a diagonal line down the middle, then drew 1/4" seam allowances around the 3 sides and measured to see what size Unit A is unfinished.