As shown below:
jupyter notebok version: 5.4.1

Same here;
Issue #244 also deals with this, but setting the padding did not fix it for me
It seems like this is a known issue, there is a pull request mentioning it #273 .
So this is a probable duplicate of #244, #203 and #273 ; In case you don't want to wait for the PR to be accepted, this:
In the custom.css file, I fixed it by changing both the div.out_prompt_overlay.prompt's and the div.out_prompt_overlay.prompt:hover's min-width and width values to 11.5ex instead of the original 14.5ex.
fixed it for me.
Thanks @BrunoGomesCoelho ,
@BrunoGomesCoelho comment is correct. I know this is closed but recently just installed Jupyter on a new system and upgraded themes. My issue was custom.css didn't contain any padding in div.output_area. I added padding-left: 16px and it resolved it for me.
Most helpful comment
It seems like this is a known issue, there is a pull request mentioning it #273 .
So this is a probable duplicate of #244, #203 and #273 ; In case you don't want to wait for the PR to be accepted, this:
fixed it for me.