Thanks for your help everyone.
I have been watering the soil using clean water from the tap (and feeding once a week), but they are outside, so get rainwater too. The marks don't wipe off, the skin is actually discoloured. I was just worried since I have healthy looking tomato plants about 2 feet away. Since no one can match the symptoms to any particular disease, I'm inclined to agree that it's something physiological, maybe a nutritional or watering issue. Must be something environment related, since only those 2 plants in that 1 tub are affected, and my 9 other Gardener's Delight plants, which are fine, were germinated from the same packet of seeds at the same time. The only difference was that I was later to plant out the 2 affected plants, and I think they are growing in multipurpose compost, whilst my others are growing in tomato compost in growbags. Although the foliage is nice and green on the affected plants, the plants in general do look a bit weedy compared to my others, with much thiner stems, fewer leaves and smaller tomatoes.