You probably ran into a rare corner case, but if it happens again, swap out the player cubes marking "10" production values with spare copper cubes. That should give you the extra cube or two needed to get to the end game.
It can indeed happen in long 2-player games, despite us putting a generous amount in the game.
I would use player markers of an un-used color to mark your production or actions taken on blue cards. The color is only really important on the game board. I would not use copper cubes, as they could easily get mixed with the resources on the player board.