Anyone ever get to a crash site, find the beacon and other stuuf, but NO ship?

Just had this happen. :(

I did have a situation where a crashed ship was 2\3rds under the ground. I could still access it though.

I had this happen a LOT at one planet I was at... I ended up going to a different system and things seem to be working normally now. I think it is a weird bug where the ship appears underground somehow. Someone on reddit claims that they even saw the ship sink underground as they approached, so this is probably what is happening. Either that or you previously visited the crash site and took the ship already, but unless you pick up every crashed ship you visit, this option seems less likely.

The very first crash site I was sent to ... was my own. I'd spent days elsewhere on the planet and was cleaning up markers. I'd flown eight minutes to get there. I got out of my ship, looked around, and said "Wait, isn't this...?" Sure enough, on the other side of the hill was the crash site where I'd started the game. No ship, of course, because it was my ship.

I think it's great that there's terrain uniqueness, that you can recognize regions even when approaching from different air and ground directions.

It happened again. I went back to my starting planet to try again to complete the fauna checklist (and succeeded). I happened on a transmission tower, it found a crashed ship--on the other side of the planet no less (six hours on foot, apparently). "Hey, this looks like...." It was once again my "birthplace". Since I'd been away on other planets the cargo drop was refreshed. I didn't test the Atlas.

I have been to a number of crashed ships that looked like they were missing only to find that they are hovering a hundred feet up in the air :)
I had to jet pack up to some of them to interact.

Got to one site still in the air above it.Saw the ship move off and disappear. Somebody got it and split? Very strange.

I found an outpost with landing pad that was half buried in a rock ridge. I used grenades to blast the rock away from the door and the interior was half buried in rock as well. I was still able to use grenades INSIDE the outpost to clear a path to the alien and the terminal. I've only seen this once and have never been able to use weapons inside a building again. But learned if something is missing it might be buried in the rock.

I've had this happen a few times, twice with crashed ships, and once with a building! Just quit and reload the game from the last save place (probably when you jumped out of your ship) and voila! The crashed ship is visible.