Are you catching on the straight seams or just the corners where several blocks intersect? If on the straight seams, your top may not be tight enough. If at the intersections, then try raising your hopping foot a TINY bit.
In the future, twirl the seams when you piece.
Here's an example:
http://laquilter.blogspot.com/2009/0...ing-seams.html
you can't always do it, but it really makes for flat tops.