Just like title says, the gantry is hitting the z-guide before it hits the Y-endstop. This causes the gantry to continuously crash into itself during Y-homing instead of gracefully stopping once it hits the end.
I received a response from the team which said that the eccentric guide should hit the endstop, but it doesn't hit it because the gantry's top guide hits the edge before the bottom eccentric guide is able to hit the endstop. Here's a picture to illustrate:

Would anyone know why this is happening? Is this a fault during my construction or a fault with the dimensions of parts?
For the worst case scenario, I can append extra material to the eccentric guide so the gantry can hit the endstop faster, but I'm hoping there's a native solution to this problem.
Thanks!
Switch the positions of the eccentric guide and the rectangular guide so the rectangular guide is on the top.
I don't recommend bending the endstop, as David and Adam mentioned earlier, the eccentric and fixed guides on the gantry need swapping around. Also make sure the the fixed guide on the tool carriage is vertical and not twisted as it will hit the guide on the gantry. Build manual has also been updated to mention this point.
I am still waiting for my printer so I am working from the photos only, but why not just bend the metal microswitch lever so it makes contact sooner.
I ran into the same problem. Switched the eccentric guide with a fixed one, still not enough. I just pasted a chunk of plastic on the Y guide so that it would hit the switch sooner
Currently, I've removed upper guide on the Z-guide so that the gantry can fully push to the end while also triggering the endstop.
Works alright, but obviously I'd like to reattach the guide if possible.