Why might pumpkin scones made on butternut pumpkin (even the smell) made someone with Irritable Bowel Syndrome [IBS] feel ill?

Smell is usually a good guide to tolerance. Reduce the amount of foods that smell ‘too strong’. But if the pumpkin is tolerated as a vegetable there must be a texture/density factor that is making the difference. I presume they were home made? If normal scones are tolerated then try different levels of dryness in the cooked pumpkin.
Often it is probably not the ingredients but the final product. Look at the nearest tolerated product and see if you can work out the texture, density, stickiness and moistness difference to work in your favour. It is also a good idea to have the frequent sips of water with food eaten. This reduces the density of what enters the stomach.