Not the first time USN has had a collision in that patch of water. It's a highly congested area.
This is one of the hardest force protection problems to crack - how do you keep threat actors away from high value assets in high traffic international straits? Without prior intelligence, large merchants are always going to be classified as a non-threat. They are simply a navigation problem to solve, not a threat to avoid or mitigate. It's not practical to maintain separation of more than a couple hundred yards max with these ships in some of the tighter areas. As the carrier, you can't really say, "500 yds and no closer" in tight areas like international straits.
It's a bit of a different story with smaller craft. There is usually host nation security that will keep small craft outside of the carrier's security zone. We are reliant on host nation for the most part.
We don't have patrol craft in this area to do surface interdiction of potential threat craft (we do have these in Djibouti, Fujairah, Jebel Ali/Dubai, Bahrain, and Kuwait), and they can't travel with a strike group. Escorts (DDGs and CGs) are too large themselves and the area is too congested for them to do threat interdiction. There was probably an armed SH-60 airborne doing nominal force protection duties.