since i can't see it in person, it's hard to say with absolute certaintly.
it looks as though the triangle around the outside edges were not big enough to fit the blocks and got stretched. the triangles are fighting the blocks for control of the quilt. the triangles appear to be winning.
take off all the triangles. if the top lays flat, then you will only need to make new ones to fix the problem.
if you still have bubbles, the next most likely cause is that your blocks came out in slightly different sizes. so the "argument" over control is between the blocks. if that's the case, the solution will be to take apart your rows and trim all the blocks so that they are the same size.
trying to do that and still make sure all the seams that are supposed to connect will line up might be a rather large pain where you sit. you might want to put narrow sashing strips between the blocks instead of joining them to each other. you will probably achieve the illusion of perfect alignment but not have to worry about it being anywhere near perfect.
if you do take your rows apart, remember to measure carefully in case you also need to cut new triangles.
would i go to all that trouble? maybe not.
first thing i would try is some extra high loft batting. cut it to the size of the square blocks and baste it to them. now, add your layer of regular batting to see what happens. it might fill in those bubbles and make them look as though they were supposed to be that way. ;-)