I have similar problem, and I hope that it is the same cause.
I created a test script that reproduces my problem.
#!/bin/bash
set -u
set -e
MERGE=${PWD}/merge
LAYER01=${PWD}/layer01
LAYER02=${PWD}/layer02
LAYER03=${PWD}/layer03
LAYER04=${PWD}/layer04
mountpoint ${PWD}/merge >/dev/null && umount ${PWD}/merge
for i in layer0{1..4} merge; do
 rm -rf ${PWD}/${i}
 mkdir -p ${PWD}/${i}
done
# layer01 / mkdir
mkdir -vp ${LAYER01}/bar
# layer02 / rmdir
mount -t aufs -o br:${LAYER02}=rw:${LAYER01}=ro+wh none ${MERGE}
rm -vrf ${MERGE}/bar
umount ${MERGE}
tree -a ${PWD}/layer* ${MERGE}
# layer03 / mkdir
mount -t aufs -o br:${LAYER03}=rw:${LAYER02}=ro+wh:${LAYER01}=ro+wh none
${MERGE}
mkdir -vp ${MERGE}/bar
umount ${MERGE}
tree -a ${PWD}/layer* ${MERGE}
# layer04 / touch and rmdir
mount -t aufs -o
br:${LAYER04}=rw:${LAYER03}=ro+wh:${LAYER02}=ro+wh:${LAYER01}=ro+whnone
${MERGE}
ls -la ${MERGE}
touch ${MERGE}/bar
ls -la ${MERGE}
rm -vrf ${MERGE}/bar
# deleted ${MARGE}/bar. But exists.
ls -la ${MERGE}
I checked with folloing kernels.
 - debian kernel(3.16.0.4) + aufs package
 - vanilla(4.2.1)+patch(aufs-4.2-20150928[standalone]) .
The other information is listed in the following.
I want to solve this problem.
You tell me if that there is information required for the other .
debian-jessie:~/aufs-test# cat /proc/mounts
sysfs /sys sysfs rw,nosuid,nodev,noexec,relatime 0 0
proc /proc proc rw,nosuid,nodev,noexec,relatime 0 0
udev /dev devtmpfs rw,relatime,size=10240k,nr_inodes=61036,mode=755 0 0
devpts/dev/ptsdevptsrw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000
0 0
tmpfs /run tmpfs rw,nosuid,relatime,size=101112k,mode=755 0 0
/dev/sda1 / ext4 rw,relatime,errors=remount-ro,data=ordered 0 0
securityfs /sys/kernel/security securityfs rw,nosuid,nodev,noexec,relatime 0
0
tmpfs /dev/shm tmpfs rw,nosuid,nodev 0 0
tmpfs /run/lock tmpfs rw,nosuid,nodev,noexec,relatime,size=5120k 0 0
tmpfs /sys/fs/cgroup tmpfs ro,nosuid,nodev,noexec,mode=755 0 0
cgroup /sys/fs/cgroup/systemd cgroup
rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/lib/systemd/systemd-cgr
oups-agent,name=systemd 0 0
pstore /sys/fs/pstore pstore rw,nosuid,nodev,noexec,relatime 0 0
cgroup /sys/fs/cgroup/cpuset cgroup rw,nosuid,nodev,noexec,relatime,cpuset 0
0
cgroup /sys/fs/cgroup/cpu,cpuacct cgroup
rw,nosuid,nodev,noexec,relatime,cpu,cpuacct 0 0
cgroup /sys/fs/cgroup/blkio cgroup rw,nosuid,nodev,noexec,relatime,blkio 0 0
cgroup /sys/fs/cgroup/memory cgroup rw,nosuid,nodev,noexec,relatime,memory 0
0
cgroup/sys/fs/cgroup/devicescgrouprw,nosuid,nodev,noexec,relatime,devices
0 0
cgroup/sys/fs/cgroup/freezercgrouprw,nosuid,nodev,noexec,relatime,freezer
0 0
cgroup /sys/fs/cgroup/net_cls,net_prio cgroup
rw,nosuid,nodev,noexec,relatime,net_cls,net_prio 0 0
cgroup /sys/fs/cgroup/perf_event cgroup
rw,nosuid,nodev,noexec,relatime,perf_event 0 0
cgroup/sys/fs/cgroup/hugetlbcgrouprw,nosuid,nodev,noexec,relatime,hugetlb
0 0
systemd-1 /proc/sys/fs/binfmt_misc autofs
rw,relatime,fd=22,pgrp=1,timeout=300,minproto=5,maxproto=5,direct 0 0
hugetlbfs /dev/hugepages hugetlbfs rw,relatime 0 0
debugfs /sys/kernel/debug debugfs rw,relatime 0 0
mqueue /dev/mqueue mqueue rw,relatime 0 0
rpc_pipefs /run/rpc_pipefs rpc_pipefs rw,relatime 0 0
none /root/aufs-test/merge aufs rw,relatime,si=281b3cc259ea3b9 0 0
debian-jessie:~/aufs-test# find /sys/module/aufs/ -type f | xargs head
==> /sys/module/aufs/parameters/brs <==
1
==> /sys/module/aufs/parameters/debug <==
0
==> /sys/module/aufs/parameters/sysrq <==
a
==> /sys/module/aufs/parameters/allow_userns <==
N
==> /sys/module/aufs/version <==
4.2-20150928
head: cannot open â/sys/module/aufs/ueventâ for reading: Permission denied
debian-jessie:~/aufs-test# cat /proc/mounts
sysfs /sys sysfs rw,nosuid,nodev,noexec,relatime 0 0
proc /proc proc rw,nosuid,nodev,noexec,relatime 0 0
udev /dev devtmpfs rw,relatime,size=10240k,nr_inodes=61036,mode=755 0 0
devpts/dev/ptsdevptsrw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000
0 0
tmpfs /run tmpfs rw,nosuid,relatime,size=101112k,mode=755 0 0
/dev/sda1 / ext4 rw,relatime,errors=remount-ro,data=ordered 0 0
securityfs /sys/kernel/security securityfs rw,nosuid,nodev,noexec,relatime 0
0
tmpfs /dev/shm tmpfs rw,nosuid,nodev 0 0
tmpfs /run/lock tmpfs rw,nosuid,nodev,noexec,relatime,size=5120k 0 0
tmpfs /sys/fs/cgroup tmpfs ro,nosuid,nodev,noexec,mode=755 0 0
cgroup /sys/fs/cgroup/systemd cgroup
rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/lib/systemd/systemd-cgr
oups-agent,name=systemd 0 0
pstore /sys/fs/pstore pstore rw,nosuid,nodev,noexec,relatime 0 0
cgroup /sys/fs/cgroup/cpuset cgroup