ouch... did you leave the Axoloti UI running in both occasions? when you disconnected the board, did it stay live or disconnect correctly?
unfortunately the truth is , Apple have screwed up here, a user land application should not be able to cause a kernel panic.
BUT unfortunately, the reality is, with 10.11 they rewrote the USB stack and it has caused endless issues, its got better as the minor updates have been released, but its still no where near as stable as 10.10
Both my Eigenharp and Soundplane have similar issues, basically if you dont close the associated application El Capitan is likely to crash. (though thats down to isosychronous data, which is not used by axoloti), Ive been sending in detailed crash reports to Apple since the first release of 10.11, and only seen slight improvements since then.
the only thing we can check is the disconnection is properly dealt with, as its imperative in 10.11, you dont continue to attempt communicate with the device if its disconnected (I fixed this on the Eigenharp software, and it help alot).
what we are unlikely to be able to prevent, is if you put the mac to sleep whilst the board is connected and running, thats possibly going to cause issues.
also it may not be the axoloti code at all the axoloti appears as a core midi device, it could be this code that is crashing.
you could verify this by allowing axoloti to continue running the patch, by stopping the UI, and then doing a sleep... if it still kernel panics, then its unrelated to the axoloti UI.
sorry, might sound like 'excuses' but having been through this with the Eigenharp and Soundplane software, I know there a few critical usb bugs still in 10.11, so its possible we may have little control over it.
Personally, Im hoping Apple have done some serious rework of the USB stack in 10.12, and thats why we have seen only minor improvements in 10.11, but i wont hold my breath.
(BTW: Id recommend users do not upgrade to 10.12 until the picture is clear on compatibility, Apple do not have a great track record these days with betas and initial releases, things tend to break)