@Lowena if the four squares in the centre are all the same fabric there is absolutely no reason why it shouldn't be just one big square.
As for using HSTs for the geese, there IS a reason (it's easier for you) to do so, so go for it.
BUT, I still think that you should use a ruler to check on the finished sizes of all the squares because something is not right. If everything was as it should be you wouldn't have the problem you have.
Accuracy of cutting and accuracy of sewing are the two key factors to getting good patchwork blocks.