The AI's and the player's automated survey ships have always ignored defended anomalies. With the addition of Precursor Anomalies, those have been ignored also. The most recent update to the beta 1.6 version with Mercenaries is reported to have fixed the AI so that they will survey defended anomalies. No mention was made about fixing the player's automated survey ships.
In the game I am currently playing as the Arceans, the AI survey ships are surveying all protected anomalies while my automated survey ships are not.
The problem is that the AI is treating the anomalies as if they are not defended. An AI survey ship will go into a protected ship graveyard and finish with no damage. When I manually send my ship into one, it always suffers some damage unless it is an Iconian ship with Healing Hulls. Even worse, when an AI survey ship goes into a heavily protected Precursor Anomaly, it also finishes with no damage. I have to send in my survey ship with enough other ships to have a hope of surviving.
Even stranger is what happened when I tried to prevent the surveying of a Precursor Anomaly by an AI survey ship. I managed to get a military ship to stop on the anomaly the turn before the AI ship got there. When the AI ship did get there, it moved onto the same tile as the Precursor Anomaly and my ship and surveyed the anomaly (the anomaly disappeared). The AI survey ship was not damaged, and its turn ended with it still on the same tile with my military ship. There was no war declared and no battle with my ship. I tried to form a fleet with the two ships, but it didn't work. Here are some screenshots showing the two ships in the fleet management window.
The next turn the AI survey ship moved on without a problem or damage.
I have submitted Ticket #GAW-717-31234 with a save the turn before this occurred.