I don't know if anyone else has encountered this yet, but there seems to be an issue with the fruit appearing on trees to show they're available for you to obtain. You have to actually get close enough to interact with the tree and only then will you be able to tell if you can harvest the resource or not. I've tried restarting the game to see if that would fix the issue, but that does not seem to be the case.
Also to note, I've noticed that this only really occurs if I gather later than usual. In the case for me here in West Aelio, I didn't go into the area until approximately 23:00 last night to gather (12/07), and returned to the area today (13/07) at around 14:50. I wonder if when SEGA first addressed the bug with resources not respawning correctly and made their adjustments, if they overlooked the timing for the graphic to display showing the fruits ready to be harvested on the trees.