Firefly makes a Malayan Tiger Gate trap (a branch with sharpened spikes tied to a tree. The branch is pulled back so that it will drive the spikes into whoever springs the trap). This might point to Firefly having received military or Special Forces training.
Even before Snake-Eyes' disfiguring injury we are never able to see what he looks like, thus maintaining his aura of mystery.
Scarlett reveals her feelings for Snake-Eyes.
The Everglades chase seems to be missing some panels. On page 11, we are left with the Joes and Cobras facing each other down in a Mexican face-off. Next mention is the very last panel of the comic with Cobra Commander saying that the Joes have disappeared again. There is no intermediate progression of the story. One panel they are there and the next, they have disappeared.