There are certainly spells that could cause that but only as the spell's intent, not as a side effect- generally, cosmetic spells are designed to allow someone to pretend they're someone in particular or at least a specific race, gender or some such, but they could be used to create something like Edwin is describing with a few tweaks. The problem is that such spells are non permanent and would need to be recast. A very skilled caster could possibly have them last for days per cast, possibly even weeks, but it would be single target, so if the other pilgrims are the same, each would have had to have the spell cast on them individually. Possible, but difficult logistically speaking and something they'd notice being done pretty easily unless the pilgrims are a lot sneakier than the party has given them credit for.
As for shadows in the eyes... wayang are a sub-race of halflings that have adapted to the Plane of Shadows to the point that they often have murky shadows drift across the pupil and iris of their eyes. Some tieflings might have shadow effects in their features as well. But both of those would have other, very noticeable traits as well, such as being half this size, horns, tails and having non-human shades for their skin and hair.
Now, if those shadows are actually some physical object instead of being actual shadows caused by magic, that's another matter. Again, tieflings could have such strange features but would have other noticeable traits. Certain kinds of gensai might have crystalline eyes, and thus facets and flaws in their eyes that could create shadows but their skin and hair would also have a crystalline, or at least mineral/metal-like, appearance.
In fact, Cy can't think of any race that would have such an effect that wouldn't have other, much more noticeable traits as well. And given one of his last tests before this whole quest thing happened was on magical humanoids, he feels pretty confident about that conclusion. Pretty good score on it too. On the other hand, that simply implies this is not a normal feature of whatever race they are (which implies in turn that they're humans as they said). So... perhaps a disease, magical or mundane. Or mayhap a curse or rather strange scar from a magical attack? An effect, intentional or otherwise, of some kind of ritual?
Perhaps trying to cross-reference this with other clues might lead to some kind of answer... What else do they know about the pilgrims that seems off, besides strange eyes and poor sense of direction?