When I first started quilting I had the same problem. I (eventually, lol) discovered that as I got to the end of the block I was piecing I let the fabric slip, ever so slightly, to one side and it ended up squint. Then, when I went to put the blocks together, everything would be 'off' just that little bit. Now that I mostly chain piece (and pay more attention to the end of stitching), my blocks are much better.
Also, someone told me, once you've nested your seams, to pin at a 45 degree angle, rather than 90 degree and leave the pin in until the foot is just on it before removing. This has worked for me.
(I don't leave pins in any more - all I'm saying is - I'm glad I wear glasses for close work
)
Good luck!