This must have been designed by a intern or something because pretty much everythyng is wrong with this design!
So the reason that i think this is causing a problem is the sharp rise time in the ripple on the 5V output. That fast risetime will try to quickly charge any capacitance on the other side of the USB hub protection circuitry, once the load is big enough the spikes in current will exceed the trip point and make it go into overcurrent mode. The reason it happens on all ports is that the Raspberry Pi 3 uses a single 5V high side switch with built in protection to switch all 4 ports (Cost saving most likley). The pins on the USB hub are wired together so that a overcurrent signal is sent for all 4 ports, that's why it will report an error for all ports. I know about this because i had to reverse engineer that part of the circuit some time ago.
Lets start listing whats wrong with it:
- The HV clearance is very important for PoE compliance as you can get massive spikes on long ethernet cables. That slot is doing absolutely nothing due to the copper fill mistake and im sure the clearances are not to spec.
- The fact that plugging it in gets in the way of the GPIO header is a major fail. You could have used one of those long pinned troughhole headders that arudinos and so many other Pi Hats use.
- That tiny 4 pin connector should have at least had some large copper pads with vias to hold it down (Or even better just use troughhole)
- 250mV of ripple is pretty bad, but its made even worse by that sharp rising edge in it
- This can NOT run reliably at 130°C on major semiconductor components.
- They did not use the opportunity of a copper fill around the diode to cool it (Not even giving it vias to help drain the heat away)
- The layout is a bit meh around the secondary side as it has a fair bit of current loop by the time it gets rectified to DC (These are very fast swings in this topology)
- The common mode cap over the isolation barier has a really long way around. This will likely make the board radiate radio interference like crazy
- That common mode current also has two paths, each one around the fan, not a good design with fast transient currents
- Output voltage goes out of control with no load calls for at least some sort of zenner diode to keep it within sane limits (This topology can really run away badly with no load)
- It should survive such an output short circuit just fine as im sure a lot of people will eventually short out the 5V rail trough some stupid mistake (Most regulator designs are short circuit tolerant these days)