System-wide Vulkan layers definitely cause chaos. I remember unit tests for our renderer crashing on some machines and not on other nearly identical ones. The culprit was a Vulkan layer installed by a video capture software. It had a hard limit of 16 Vulkan instances that it could keep track of before overflowing an array and crashing. But our tests would recreate the Vulkan environment from scratch for each test, which is fairly unusual for a Vulkan application, to be fair.

In the end, we added the list of loaded Vulkan layers to the diagnostic log of our software to help customer support spot fishy ones.