I've posted or seen posted about this before, mostly thinking it was just an annoying graphics glitch, but I've noticed today that it actually goes further.
The bug of `the second marble' find not showing up unless you refresh was bad enough when it cost you a wasted geo search, but I've discovered two addition effects which go beyond just the graphics and makes this a genuine bug:
a) If the deposit is not showing the mason does not work it ( I've clicked on the work yard and his pathing goes to a deposit much further away, but on refresh he immediately goes to the now showing deposit.
b) If the neighbouring deposit is found but not showing ( as happened in sector three today ) and then the deposit runs out, the two deposits appear seconds later with 100 marble in the just expired deposit and 240 marble in the found but hidden deposit.