At the end of the Castle Clinton side mission, the player is required to clear the area of enemies before activating an echo to finish the mission. After clearing all the enemies inside of the location, the player can still be noticed by enemies that are outside of the mission area. The player cannot get to these enemies to clear them so the echo remains inaccessible. Either new enemies are spawning unintentionally or they are meant to come into the mission area but are getting into conflict with the allied NPC's outside the area available to the player.
This has been reproduced twice by myself.
Two workarounds include: 1. Having a coop partner fast travel outside of the area to manually clear the enemies and then the other player finishes the mission.
2. Letting the allied NPC's outside of the mission location fight and (hopefully) take out the enemies. This can take a lot of time and is not ideal.
Unfortunately, since side missions are not replayable, video evidence cannot be provided.