Me and my friend are playing through the game and on (I believe) 3 separate occasions, he has on his compass seen a safe house that is no less then around a mile away. his latest journey included running from the north end of the farmlands, towards the lighthouse on the north east shore. we don’t know why he sees them but i never can. if there is an explanation or a know fix/cause i would personally love to know
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Did he visited those SH’s on his own? Did he “saw” them at other lobbies?
Might be 'cause of mess between his more advanced save and your’s. Or he just plain knew where to walk.
I had those “ghost” safehouses after I 100%'ed my realm and began visiting multiplayer as guest. Some things are carried over to your realm from others too as well.
No we are playing through it all on my world and He told me himself he has only just entered the farmlands on his own world. I’m the only person he plays this with
I had this in singleplayer once, too.
I started following it at the homebase towards lower west and gave up somewhere next to the refuge in farmlands. 
I don’t know how far I have had to go on, to reach the showed savehouse…
There was a case for me, when I had to cross three regions to a certain safehouse, so it could finally vanish from my compass.
Still, mess with safehouses appear when multiplayer is involved. More often so if same realm has multiple sessions.
Like I said - I’ve had “clean” compass (after 100%'ing my realm solo), went MP, then got a bunch of persistent SH’s, which won’t go out until I visit them (including already discovered once).