It also could be that the pattern in the book is not the right 100% perfect angle. Did you trace the pattern off? Did you use a copy machine? The size of the petal is very important... if it's a smidge too wide or not the right angle exactly, the end result will not lie flat. So you need to check that too.

Margarita, why don't you make a template of the correct FINISHED size that each petal should be and see how that lines up with your stitched petals.
If the finished size does not match your accurate template, you seam allowances are not correct.

Because your stitched units are too large, it might be possible to make minute adjustments to each seam to make it lie flat, but it would be better to figure out how to make the seams the right size to begin with.

Maybe reviewing my "test" for seam allowances would help? http://good-times.webshots.com/album/569415726bHNKHF

This is frustrating and embarassing! I am doing some dresden plates for a quilt, using the pattern from Alex Anderson's book Neutral Essentials P.28. I have made 3 so far and each time no matter how careful I am there almost seems to be an extra "petal" and the thing will NOT lie flat. I counted the petals and there are only 12 as required. The first time I unpicked a few and corrected the seams, the next time the seams look right to me so I just folded it in half and machined across the extra. Painful but the quilting police do not live near my house, however they are in my head and I cannot bear this result. Is there a trick to this or what can I be doing wrong?