Fear not, it likely is not a bug! There are some effects in the game that can restrict the placement of dice. For example, the Dragon does not allow black heroic dice in skull boxes, and the Phoenix's Den 3rd floor does not allow black heroic dice in armor boxes.

If you're sure there was no effect in play like this, please send along a detailed description of the situation and a screenshot if possible to help us diagnose the problem and find a solution.