some fabric stretches more than others. If you use steam and/or iron (instead of just pressing) the seams, sometimes the fabric gets distorted. May also be a reason to prewash. Also, I have less problems with higher quality fabric
take your time
learn to tug a bit, scrinch (my own personal term) a bit to make seams line up
use pins (I don't but I am not that particular about my seams)
press seams the so that they lock when you put them together.
In the end, remember that quilting is supposed to be fun!