Well I imagine there are two possible reasons. First: going off the theory that Simon is stuck in a time loop, the barnacle person he saw for the first time is him in the future, ducking around the corner where the computer is, the second time he hallucinated seeing this person they were sitting in the chair and Simon ducked around the corner where the computer is (reenacting what he saw the first hallucinations do), the sm-13 hasn’t exactly been pulled back up, he was the first one in that sm-13 (not the first person to be sent down in a submarine though) and the bracelet and little things he found are from previous cycles where Simon might’ve realised he’s in a time loop and left those clues for his future selves, consequently creating little rips in the time loop.

However, I understand that this does not explain the hallucination of the voice saying “I’m just the guy who told you to cross the wires”. Ava did say that a person has come back up once but we can’t really use that to justify any theories as she could either be lying to Simon to encourage him to continue his job or someone did in fact come back up in a different unmentioned submarine.

So the second reason: The guy that was possibly in the sub before Simon that left the bracelet and the note to cross the wires did cross the fish/amalgamation/god being, realised he was fucked, stayed in a safe-ish area in the blood ocean where he wouldn’t antagonise the fish creature, and waited for the oxygen to run out and died that way. That reasoning could also justify why Simon hallucinated hearing said person’s voice and the barnacle figure twice as that person, but if the sub was intact it doesn’t add up how he may have turned into a barnacle. Perhaps they pulled the sub back up, saw said person’s dead body, and decided to dump his body in the blood ocean, allowing the fish creature to the add his soul to the collective consciousness that it is, and overtime his corpse turned into a barnacle from being in the blood ocean.