What is the best way to visualize data that is over 100% capacity
If you want to see small numbers and large numbers on the same chart, you can use a log() scale for the y axis. This will work for bar charts, or other types of charts. Log scaling will show more details than linear over a larger range. Just need to point this out to the user as they may be used to seeing linear scales. For something that changes over time, it can be helpful to show a time based plot, with any data over the limit in red and the data under in green or blue. Also you can add a horizontal line showing the cutoff value.
Example:
Linear vs Log

Flag with red points including a horizontal line to show the cutoff