Numbers does the best it can with the information you give it. If you ask for Error Bars, Numbers will calculate the standard deviation for the series and assign that calculation result to each of the bars in the series.
If each of your values represents some statistic that in itself is accompanied by a standard error, that's another thing, but Numbers doesn't know what the error values are unless you tell it. The way to tell Numbers what the error bar values should be in these special cases is to use Custom values.
Here's an example:
I like to use the Scatter Chart, but you will find similar controls for the bar chart.