It could have been an abscess. I have had horses come up with abscesses after rolling and getting barbs off of a sandbur or a quill from a cactus in their skin. Stuff like that, you wouldn't notice it during regular grooming because it broke off underneath the skin. You only really notice it when a small knot starts to come up where it's trying to fester out.
If that happened, where it's located, even if it burst, it wouldn't have drained like it needed to and would have been very prone to further infection.