

The incompatibility was discovered by Plugable (via 9to5), who found that their TBT3-DP2X and TBT3-HDMI2X graphics adapters were not compatible with Apple's new MacBook Pros because they use a controller chip from Texas Instruments. As a result, Plugable will be postponing its upcoming Docking Station as it works on a compatibility solution.
Because some existing or soon-to-be available Thunderbolt 3 accessories may not be compatible with the new MacBook Pro, customers who are looking to purchase docks, adapters, and other products should double check with manufacturers to ensure compatibility.Update 11/1/16: Apple has chosen to prevent Thunderbolt 3 devices using currently available controller chips from Texas Instruments from enumerating and functioning on the 2016 MacBook Pros. All current Thunderbolt 3 peripherals which use this controller chip are incompatible with the new 2016 Thunderbolt 3 MacBooks (To our knowledge, this includes all currently available Thunderbolt 3 devices including our TBT3-DP2X and TBT3-HDMI2X graphics adapters. Our Thunderbolt 3 cables do not require this chip, and therefore are compatible.)
Because of this, we've made the difficult decision to postpone our TBT3-UD1 Docking Station as we evaluate what is necessary to make this docking station MacBook-compatible. Our Flagship TBT3-UDV dock with Power Delivery/Charging is using the next generation controller chip from TI, and will be compatible with the 2016 Thunderbolt 3 MacBooks.
Many products on the horizon newer Thunderbolt 3 chipsets and won't be affected, and it's also possible Apple could push a firmware update to add support for accessories with the older Texas Instruments controller.
Update: Plugable has provided MacRumors with more information on which Thunderbolt 3 accessories are supported by the MacBook Pro and which are not.
The version of OS X on the new MacBook Pros (late 2016) will not work with existing Certified Thunderbolt 3 docks and adapters (released prior to November 2016). These existing devices use Intel's Thunderbolt 3 chipset (Alpine Ridge) in combination with the first generation of TI USB-C chipset (TPS65982).
Apple requires the 2nd generation TPS65983 chipset for peripherals to be compatible. Certification of solutions across different device types is still in-progress for this 2nd generation chipset. From the Plugable product line, our dual display graphics adapters for DisplayPort and HDMI (TBT3-DP2X and TBT3-HDMI2X) are affected and are disabled by OS X on the new MacBooks. So we offer these products as Windows-only Thunderbolt 3 devices until a future hardware update. Our Thunderbolt 3 cables do not require this chip, and therefore are compatible.
We've also made the difficult decision to postpone our TBT3-UD1 Docking Station to update to the TPS65983 chipset and re-certify to make this docking station MacBook-compatible. Our Flagship TBT3-UDV dock with Power Delivery/Charging was already planned to use the next generation controller chip from TI, and will be compatible with the 2016 Thunderbolt 3 MacBooks.
Article Link: New MacBook Pros May Not Be Compatible With Some Early Thunderbolt 3 Devices [Updated]