When creating a world, you can turn on a "Bonus Chest", which gives you a few saplings, some logs, a couple tools, and some food. However, with Pixelmon installed, it is completely overwritten with pokeballs, great balls, and ultra balls.

Hey,

I was able to confirm this (https://imgur.com/a/i3tO8wi), however, this is an intentional design. And I quote, "This is intended. There is a chance it will give the three balls, rare candies or even an EXP share."

-Swifty

While the fact it gives you the balls (was unaware of the other stuff, have not encountered those myself) is good, and I'm not saying the fact it's there is an issue, it's the complete overwriting that feels like a bug and what I was reporting.
Perhaps it would be better to make it a suggestion to make the balls and exp items additions rather than overwrites?

Heya! Just wanted to update - It was decided to change the weights for pixelmon items AND make sure both pixelmon and minecraft items can be found in the bonus chest. This change will be in the next upcoming version :)

Thanks!