Constant repeated pressure in exactly the same way for an hour plus in inherently fairly stiff uncomfy tight shoes will do that, unless you pay loads for a bike fit and shoe matching.
If you think about it when you’re on the road there’s more factors at play:
– Regular micro unweighting of a foot when cornering, or changing direction etc
– More changes in cadence – even a small amount
– The big one for me is that on the road you have to pay more attention to everything around you. Scanning the road, adapting to wind, avoiding potholes, checking behind for cars etc – everything that you don’t need to do on the turbo. So little tiny uncomfortable niggles are really amplified when the only thing you’re focusing on is a screen in a boiling hot room.