I may have an unpopular opinion, but I didn't think they made as much of a statement about racism as they did about "us vs them". I noticed that they were not racially diverse, but they are Aliens. Perhaps that is how the race is. She immediately blocked the Doctor because his approach was so brusque. Ruby tried to be nicer so wasn't quickly dismissed. Pepper was shocked be cause they were in the same room. Because these aliens never interact together outside of the bubble but it was clear Ruby and the Doctor were. Even though the Doctor and Ruby offered to take them away, it seemed more of an us vs them situation and Pepper wanted to stay with the us.