The datasheet for CB3LV-3I-16M0000 says the bypass cap (C1) should be
between pins 2 and 4. On the layout it's connected to the ground plane
rather than directly to pin 2. Same issue with C2.
Likewise the bypass caps on the AVR should be near the power pins.
In fact we should probably update the schematic to put one 0.1uF bypass
cap on each power/gnd pin pair. I.e. 14/15, 24/25, 34/35, 44/45, 52/53
& 60/61