It's a leftover from when Prometheus was supposed to be a direct Alien prequel. If you pay attention, the engineer's corpses have holes in their chest as well. It makes no sense in the current context of the movie.
All these things are just leftovers from what the movie was really supposed to be: An Alien prequel that was supposed to open a new universe of possibilities with the trip to the engineer's homeworld at the end of the movie (the ending didn't change).
Instead of have an alien prequel and follow up movies expending the engineers lore, we ended up having a first movie that focused neither on the engineers nor the aliens and a sequel that tried to be an alien movie, ditched the engineers and instead focused on David.
The original concept was really good, but Ridley is just fucking things up with each new movie and it's clear he doesn't really have a clue where he wants to go next.
It's interesting to note that in this early script, the engineer furiously killed the crew because waking up from stasis doomed him, since he had an alien in his chest. The engineer was also much bigger than what he ended up being in the movie, thus looking more similar to the pilot in the first alien movie (it was supposed to be him).