I completely understand what you're saying, and have had the same issue, and I know it wasn't because the quilt was wonky or wavy to begin with. I *think* that the problem occurs because I wasn't careful enough to keep the sides of the quilt completely straight, so that they started to angle in by the time I was at the bottom. That meant the extra fabric at the bottom had to be eased in, and the bottom wasn't as wide as the top.
The other thing that might be happening is that the quilting stitches cause the quilt to contract somewhat, so it looks like there is more fabric at the bottom, whereas there really isn't - it just hasn't been quilted yet. To take care of that, I try to unpin the bottom part of the quilt top before I get too close to finishing, and then pin the sides of the top to the batting and backing. That seems to keep it where I want it to be so the bottom is square.
Now that's what I've done... probably not the right thing... I'd love to see a video of someone doing it. I don't remember ever seeing a video of someone finishing the very bottom of a quilt.