when my joints are off, the first thing i do is check the seam allowances on the sewn pieces to be joined. if they're off, i fix them. if they're the right size (usually 1/4") the fun starts.
i've recently started pinning across the intersection, so my pins run parallel to the presser foot. i put the pin about 3/4" from the edge so i don't have to take it out when i get to it. that also lets me check the join from both directions.
when they're really stubborn, i pin across the join, then once "up and down" on each side of the join. i sew slowly. sometimes i have to remove the pins, sometimes not.
when they're really, really, really giving me fits, i pin and sew just the joins and don't "fill in" the whole seam until the joins are right.
if none of that works i either induce self-hypnosis so i don't see the wonky bits any more or i set them aside and move on. then i make replacements for the ones that wouldn't go together properly. i set them aside to use them later in a scrap quilt, or - if i don't have enough fabric to make replacements - take them apart and reassemble until they fit together the way they're supposed to.
needless to say, i spend a lot of time in a transe. AND my scrap bag is bursting with orphan sections of wonky blocks. :shock: