Part of the trouble you all are experiencing is that the “bran” or “whole grain” aspects are cutting the gluten strands while mixing.

When you are using that combination, try mixing at a slower speed or for shorter time do it is gentler on the dough.

If you are adding whole grains as one ingredient, try waiting to add them till after the start of mixing. This will give them less time to cut the gluten.

This also applies to adding sprouted grains. Soaking the grains longer (waiting the full 24 hours and not cutting the soak short) will soften them so they aren’t as harsh on the flour.