I also had some thoughts on the prevalence of the X markings but it went in a kinda different direction? Putting this under a read more for both length and spoilers:
The idea I was going with is that these Xs are pretty much shorthand for "there is information here/this is important".
The small Xs Simon is shown drawing on the map to mark where he is -> the map allows him to know where he is, giving him information of his location and his distance to points of interest.
The X tape in the camera, and later the flesh-blob growing in a similar shape* -> The camera is used both to see/discover things outside the SM13 and, temporarily, as a light source so Simon can see what he's doing. Both tied to the sense of sight and "gaining information about one's surroundings"
The Eden symbol, which looks like a weird X, engraved on the side of the terminal -> conceals both the pendant (which, in a way, starts to give the viewer some info about Eden and the previous convict) and the instructions to start the terminal (where Simon finds information about the previous convict + lets him access the data in the SM8 black box) (also this could be a reach but the message being "cross the wires" instead of, say, "connect the wires" brings the shape of a cross -- as in, an X shape -- to mind, which could be something)
The scar on Simon's neck: I didn't really notice it at first, and it doesn't fit in the theory like the other elements in the list, BUT I think it's on the same side of his body as the arm he loses later/the side where most of the mutations are seen -> it could be a "this is important" signal, foreshadowing his transformation.
As for the tape in the pendant, I didn't really catch it either during the movie and I can't find any photos where the pendant has tape on it, but I'd go with something similar to the previous point -> marking the pendant as something important/significant (maybe foreshadowing the part where it seems to grow roots in the Light-induced hallucination sequence + the "Simon mutates into a tree" ending interpretation? Idk about that last part really, I'm just connecting dots)
So yeah, that's my guess on the symbolism of the X shapes in the movie. It's kind of a stretch in some parts but I think it does hold up, especially when you consider the saying "X Marks The Spot" and how X shapes are often used in popular culture to indicate something important (esp. in a map)
* the fact that the flesh growth was shaped like an X too was most likely itself a call-back/parallel to the tape earlier, but that worm belongs to another can I won't open on this post
