After getting the third guild upgrade and having three items in the three locker slots before, they got cloned into the other empty locker slots upon relog.
Meaning I had a guild hall lvl 2 with three items in the three locker slots.
After I upgraded the hall to lvl 3 I had 6 locker slots, in three of those were the old items from before. The other three were empty like they should. After I relogged the three items had suddenly duplicated into the empty locker slots meaning I had 2 of each of the original items.