did you wash your fabric first? it goes bak to its "natural" shape after being washed and dried. very frequently the ends won't line up "nicely" after a fabric has been washed.
sometimes the fabric is pulled crooked when it's wound on the bolt.
i've learned to check for grain lines before buying fabric. if it's printed off-grain, one has to live with it.
when they cut the fabric, they are (supposed to be) cutting it perpendicularly from the edge of the fabric, as it's on the bolt.
i usually cut my fabric from the wrong side because I like to see the grain lines, but it really doesn't matter.
i also prefer to cut my long strips parallel with the selvage instead of from selvage to selvage. that way i usually get at least two sides that have a true grain.