Over-kneading whole wheat bread dough results in a tough, dense loaf because it damages the gluten structure and releases too much glutenin, making the dough slack and unable to hold its shape.
Kneading is crucial for developing gluten, the protein network that gives bread its structure and elasticity. Whole wheat flour contains bran, which has sharp edges that can cut and weaken the gluten strands during kneading. When you over-knead whole wheat dough, you excessively work the gluten, causing it to break down. This breakdown leads to a dough that is slack, sticky, and difficult to handle. The resulting bread will be dense, tough, and may have a poor rise. Furthermore, over-kneading can release too much glutenin, one of the two proteins that form gluten, which contributes to the dough's stickiness and lack of structure. The ideal kneading time for whole wheat dough is generally shorter than that for white bread dough.
To avoid over-kneading, use the windowpane test. Gently stretch a small piece of dough; if it stretches thin enough to see light through it without tearing, the gluten is sufficiently developed. Stop kneading even if the dough still feels slightly sticky.