Some points that come to mind
- whole wheat flour rises faster than white (https://www.theperfectloaf.com/whole-wheat-sourdough/)
- the bran in whole wheat serves as tiny knives to interrupt the gluten formation and thus it doesn’t rise as high
So the result is it’s easy to over proof whole wheat and it’s not exactly puffy to begin with. Over proofing happens when the gluten reaches its limit and the yeast run out of food. Typically there’s a bulk fermentation to grow the yeast colony and then the gluten network is reformed and the yeast is jiggled around as the loaf is shaped, permitting the second fermentation before baking.
Sugar is a pretty common ingredient for sandwich bread because it aids in browning especially when toasting it. The yeast doesn’t consume it all - but it gets pretty far. That and fats are what make a fluffy sandwich loaf - but you’re far from that with this recipe. I don’t think you really need the molasses. Particularly because it’s going to make for a faster fermentation and the gluten is already struggling to hold in the air.