This is most noticeable when cutting down trees or yucca plants. If the tree/plant has spawning partially inside of a cliff or other environmental element there is a chance that resources dropped may be lost inside the environment.
Please also note climbing a tree that has clipped into a cliff may cause the character to become stuck.
Players have reported that sometimes angling themselves correctly can cause the prompt for a lost object to show up. If this occurs players can pickup the object even if it cannot be seen.
If a player becomes stuck in graphics elements themselves they will need to restart from a previous save.
Players who have found problems with losing clay and rock underwater often find mining one bit and a time and collecting it can help ensure they catch everything.
For a good workaround please see @MestreLion’s post below!