We've reported the problem as rdar://problem/23311441 via the Apple Bug Reporter and hope that they'll fix it in a future system update.
Apple released OS X 10.11.5 on May 16th in 2016. With this update we are no longer able to reproduce this issue. It's still a little early to say, but it looks like Apple fixed the issue. Let us know if you are still experiencing the problem after installing the system update.