I assume you are using Graph Builder. There may be better ways to do this, but this should work.
I would recommend using the Value Ordering property so that each graph will have the same order on the x-axis.
Then add a column of all 1's to the table, call this column Freq. use a pre-selected role of Frequency for this column.
Now whenever you have a graph where a level is missing, add the level, but put a 0 in the Freq column. This should make it appear on the graph.
I have included a sample file with an example where level D is missing.
Dan Obermiller