This bug is caused by the residential rental and is the bug that @Gagea25 has linked above. To stop it, you will need to either remove the residential rental lot from that zone or change it to another venue type like residential or residential haunted. Then you need to play in that zone for a few days and things should go back to normal. Trees and plants will probably have to regrow too. This issue will occur in any zone that has a residential rental in it that has been played at least once. It has been around since For Rent but became a bigger issue with the Live and Death prepatch. Originally, it only affected the plants, but the patch also caused the duplicates to spawn making the situation worse. In addition, it also affects the City Living apartment venues and causes the same issues in any zone where you have fixed apartments like San Myshuno or Evergreen Harbor. It is not evident in San Myshuno since there are no plants or dig rocks in those 3 zones, but it shows up in the two Evergreen Harbor zones which do have them, and it will show up in the two Brichester zones if you have converted the dorms from University Housing to Apartments.
What is happening is that all plants and dig rocks are duplicated on top of what is already there, and the duplicates are not interactable. The original dig rocks are still there and can be collected on the normal schedule though but when you do collect them, they don't visually disappear. The plants are a little different though. There are either still there underneath what you see and can still be harvested on the normal schedule or have disappeared altogether on lot load and will grow back eventually except that they disappear again every time you travel so you are stuck having to stay on the lot continuously for the time it takes for them to regrow again. Since the duplicate is hiding the real plant, it is very difficult to see.
Hope this helps.
