Same problem here, but I did draw it as a single rectangle in the first place:
I am throwing in my full project (I will later publish it in a blog note anyhow (disclaimer, no ads no income from my blogs, only fun and expenses. Also, I sell nothing of what I make and describe in them)). I am so new to this, that some advice might come in very handy!
Beep_BRRR-2022-03-22_104557.zip (207.3 KB)
Edit:
If my layout looks strange, I am trying to make it into some sort of breadboard, even if I know from How to implement a breadboard in KiCad that it’s probably not such a good idea. But then, KiCad looks more tempting than fritzing.
By the way, I also added mounting holes where they should be (according to Universal Proto-Board PCBs 5cm x 7cm, but the DRC complained so much that I removed them. I think it was the copper fields aound the 2.2 mm holes.
Edit 2:
I discovered the arcs and lines in the USB Micro. I tried to move it to the edge of the board as it said (with fine grid), but it still complained.