I was getting the exact same issue on PC. In addition, some of the soldiers on the deck with me (including Kovic and Irish) were glitching out and sinking into the deck of the ship, reappearing in the sky and falling in a loop, like in Portal.
I restarted the checkpoint multiple times and also restarted the mission and but I got the same issue.
I worked around the issue by walking up to the guy standing in front of the ladder, jumping up into the air and firing my shotgun above his head, killing him.
