You have 8 points coming together in the center of each square. No matter what fabric you use that is a lot of bulk but flannel is definitely making a difficult situation harder. I recommend that when you join the two triangle units to make the square press your seams open and then when you join the four squares to make your block you open up the center intersecting seams like demonstrated in this tutorial
http://www.greenfairyquiltsblog.com/...lat-seams.html