It seems like printing from an SD card gives the same issues. I'm leaving the post up if I can, but moved it general. I don't know what changed before and after using OctoPi.
I installed OctoPi on my pi yesterday. I decided to print some callibration cubes to test it out. Unforntunately some layers are not looking too well, and the top layer looks rough too. Infill seems a bit on the rough side too on half completed prints. Also, the hotend seems to knock prints away from the center from time to time. Lastely, the purge line sometimes has small gaps. The final product is still around 20mm +~0.1mm, so I don't think there anything wrong there.
I've added a picture of the cube to the bottom of this post.
Different settings in Cura and reinstalling Octopi on my raspberry pi.
browser.user_agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:98.0) Gecko/20100101 Firefox/98.0
env.plugins.pi_support.model: Raspberry Pi 3 Model B Rev 1.2
OctoPrint version 1.7.3, OctoPi version 0.18.0 running of a 8gb speed 6 SD card on a Raspberry Pi 3 model B v1.2, Ender 5 Pro 4.2.2 with a microswiss direct drive kit, Marlin 18.104.22.168, Firefox, Windows 10