I can confirm this bug is still present on MacBook Pro 11,1 and latest mainline 
kernel 4.5.0,
tested on wily.

Disabling the XHC1 in /proc/acpi/wakeup does seem to prevent the immediate 
wakeups
but this at the same time disables waking up on opening the lid for me (and 
LID0 is still
enabled in /proc/acpi/wakeup).

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https://bugs.launchpad.net/bugs/1391476

Title:
  [MacBookPro11,1] Laptop wakes up while lid closed

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