The first thing to check is whether your dimensions are correct, since you reconfigured the blocks. If they are, and since you're practicing with scraps, your best option is to perfect your seams so that you produce the desired block size. Squaring a block shouldn't be necessary if you sew with scant 1/4" seams, and it adds a lot of work and aggravation when the design doesn't flow as it should from block to block. (That said, I have been known to square off a block or two, because they don't all come out perfect.)