Just checked the Roehampton site and both bessaes got an AM so it seems
From the Roehampton site:
Two of our Phragmipedium besseae were awarded today! Both received an AM (Award Merit from American Orchid Society AOS) grown by myself at...
I wouldn't worry - they seem old injuries that are resorbed, due, most likely, to the previous owner's cultural practice (likely insect or fungal). The new tissue seems fine.