That’s very strange… it should look exactly the same, because the homepage categories use the same code as the shortcode.
You can control how many in 1 line with the columns part of the shortcode.
This is 4 on one line:
[product_categories ids="5,3,87,23" columns="4"]
If you want 3 on one line, you would do this:
[product_categories ids="5,3,87,23" columns="3"]
Do you have the shortcode on a page on your website that I can take a look at?