So I don't even know if this IS a bug, but I feel like it has to be at this point. Most of my gathering locations have not respawned since day one. I wasn't able to complete the fruit gathering daily quest yesterday (the fruit didn't appear on the trees at all, but I could walk up and gather from the bottom of 3 trees but no others in the entire area, even after logging out and switching blocks many times), and I can't complete the mining gathering daily quest today. The areas that are supposed to have a lot of mining materials (the cave in South Aelio that leads to Mt. Magnus for a cocoon, and the cliff in North Aelio that a datapod tells you about for example) have only respawned 1 or 2 nodes at best in a day. I feel like this is probably a bug because of how long its been since items haven't respawned.
If its not a bug, this is extremely poor game design. It basically punishes players for exploring before they're told to go gather specific materials with EXP loss (and potentially meseta if the weekly for daily completions can't be done), and additionally screws them out of not being able to upgrade 4-star gear if they used materials to upgrade other gear. I did upgrade 3-star gear, and I felt like I needed to do that so I could get my Battle Power high enough to participate in later content. Now I can't gather enough materials to unlock on the potential on the 4-star knuckles I found.
EDIT: I feel like I should specify that I am playing on the steam version.