On the facts described it's difficult to believe it was anything else. A group of people made identical journeys, together travelling on the same train and making the same mistake with their ticketing. The tickets were checked at the same time and every member of the group was required to pay the correct fare but only the two non-white members were additionally charged a £100 penalty.
I am old enough to remember the introduction of the first Race Relations Act. Nearly 60 years later reports, stats and anecdotes like this one suggest there is still much to put right.
It can't be pleasant to be in the middle of something like this but I hope
@HeyCiao will make a complaint irrespective of the outcome of the appeal because only by challenging this type of behaviour is there any chance of changing it. And, if it is what it looks like then it almost certainly won't be just this one instance.
The Equality Advisory & Support Service (EASS) can give advice on this sort of situation and have a freephone helpline on 0808 800 0082