Human Error

Human Error is a quest in Fallout 4.

Quick walkthrough
Enter Covenant and talk to Honest Dan

Find the caravan wreckage west of Covenant

Deezer's lemonade found in the wrecked caravan will allow for further investigation

Either explore the files on Jacob's computer or transversely, with a skill in luck of 9 or higher, fix the radio in the shop owners house at the far end of town

Find the compound (next to the fishing area in a sewer)

Fight through the guards and get to the doctor, or pass a speech check and be escorted peacefully.

Either release Amelia or Agree that she might be a synth and leave the doctor with her

An alternate way to start the quest is to simply enter the sewer and follow the three previous steps.

Upon choosing wether to spare or leave Amelia, the quest is completed.

Detailed walkthrough
The fishing spot is the location of the compound. The entrance is through the door in the middle pipe down in the water.

Places to investigate:

Bookcase in the center house just inside the door. Sleeping bag between Jacob Ogden's house and the guest house. You can learn about the existence of the compound from the store owner Peggy with a Charisma check.

If you told Honest Dan about the compound, he's waiting for you inside the outer door. He agrees to follow your lead, but if you accept the compound's deal to let them kill Amelia, he'll become hostile. (Note: someone with the intimidation perk should test whether it's possible to save him by using intimidation to turn him passive again--I'm guessing the covenant will probably still just kill him, but it's worth a shot.)

If you didn't tell Honest Dan about the compound, he'll have left Covenant when you return. (TODO: find where he goes)