You could add a narrow sashing between the blocks. That way the misalignment would not be as noticeable. Yes, it would change the design but then the design you had in mind is sort of mucked up already due to the misalignment. On the other hand, you may decide that it doesn't matter that much when you put the blocks together. It will look great no matter what route you take.

I did a woven pattern from a jelly roll AND strips from stash. My strips were all 2 1/2" and I didn't realize until late in the process that the jelly roll was over-sized. Not much I could do at that point but finish it. Now I make sure to measure my precuts before they make it into a project.