Very welcome, I'm glad if I was able to help!
Im pretty new to pcb design aswell, so anything pcb related is intresting and educational to me really =)
I just had another look at your schematic and there are two things I noticed (keep in mind Im by no means an expert and dont really know what Im doing for the most part xD).
Firstly, there are a lot of open/not connected GND Pins on the MCU, to my understanding these all need to be grounded.
And secondly, you have a over voltage protector and ferit bead between VBUS and +5V (providing protection to +5V), but +5V is only used in the reset circut, the mcu itself is provided with non filtered VBUS, is this correct/intentional?
(I have only designed one pcb so far and admittedly not included anything circut protection related, so this stood out to me)
Also your columns are mostly unassigned, but Im guessing this is a result of testing the original issue.
Definitely post some updates of the project! Im very interested to see where this goes! =)