We have run tests with a number of USB-C adapters and USB products with a 2016 MacBook without encountering particular USB issues.
We're going to test the 2015 MacBook next: the USB host controller is different.

We've observed the same issue Paul found: in systems with recent Intel GPUs sometimes the internal screen does not resume from sleep when USB screens are connected.
The same happens sometimes on warm reboots and we've seen a similar behaviour logging out and in again.
This is a Sierra issue not depending on USB-C but since all MacBooks have a single recent Intel GPU, they are all potentially affected.

If you see this issue please open a bug with Apple: this is the last severe issue not yet fixed in the latest Sierra beta!

Best regards,
Carlo

Not good that you're seeing issues too but it does make me feel better than it's a genuine problem and not something wrong with my device. It's great to see you and team working on this Carlo! I managed to get my hands on another USBC adapter to USB3/HDMI/SD card etc (forgot to check the brand) but I experienced the exact same behaviour as mentioned in my previous comments.

Keen to hear how you go with the 2015 Macbook testing.

Curtis

OK so this has not been too easy for Kamil who tested here. This configuration is quite flaky in our tests.

There is definitely an issue. What we see happening connecting a USB 3 device to the Apple adapter connected to the MacBook is that sometimes only the USB2 part of the USB hub in the dock is enumerated.

Interestingly the OS then tries to re-enumerate and sometimes succeeds after 1-2 minutes. And sometimes the whole USB bus hangs. By inserting "slowly" the USB 3 cable in the adapter the chances of success increase (probably the adapter is sensible to the VBUS timing).
After noticing this, we went back to the 2016 MacBook and saw that the same was happening but the recovery is always succeeding for that model.

This is reproducible with other USB 3 devices so I'm not sure Targus could do something about it.

So not great unfortunately.

In your situation a possible workaround could be to use a USB 2 cable between the Apple adapter and the dock. This would be more reliable.
You would lose bandwidth but up to two 1080p screens it should be fine: we don't needlessly waste bandwidth as other technologies do (ahem...).

Best regards,
Carlo

Damn, not good. Happy to try what you suggested Carlo, but I'm curious as to what is the root cause here? Is this a limitation of USBC? Are there any Windows devices with USBC that exhibit the same behaviour?

In theory everything should be working OK. And it does even with this MacBook for many use cases.

However I can imagine that USB C, especially when the new "alternate modes" are used to carry other completely unrelated signals like video or Thunderbolt, is very new and may have teething issues for some use cases.
In this case the issue may be in the USB C adapter, in the MUXes that separate video out or on the host controller. The next step would be to connect a USB analyser between the adapter and the machine but I suspect the issue is probably in the MUXes and relative logic.

This is just my personal theory given the evidence so far.

Regards,
Carlo