Consecutive COPY operations causing "layer does not exist" error in 18.06-ce

[fractos]

Description

Seeing a problem with the following Dockerfile on 18.06-ce on Amazon Linux ECS-optimised build, with
Docker using lvs for its storage, with consecutive COPY commands causing "layer does not exist" error.

Steps to reproduce the issue:

1. Using the following Dockerfile:

FROM microsoft/aspnetcore:2.0

RUN apt-get update \
    && apt-get install -y nginx gettext-base python-pip \
    && pip install awscli \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

ENV LISTEN_PORT 80
ENV PROXY_TARGET_HOST 127.0.0.1
ENV PROXY_TARGET_PORT 5000

RUN mkdir -p /var/log/nginx && \
    ln -sf /dev/stdout /var/log/nginx/access.log && \
    ln -sf /dev/stdout /var/log/nginx/error.log

COPY etc/api.nginx.conf /etc/nginx/conf.d/mysite.template

COPY API/bin/Debug/netcoreapp2.0/publish /opt/app
COPY API/appsettings.json /opt/app/
COPY API/log4net.config.xml /opt/app/

COPY etc/run-site.sh /
RUN chmod +x /run-site.sh

ENTRYPOINT ["./run-site.sh"]
CMD ["API.dll"]

2. docker build -t my-org/my-image:my-tag -f Dockerfile.test .
3. Same results with adding --no-cache

Describe the results you received:

...
Step 8/14 : COPY API/bin/Debug/netcoreapp2.0/publish /opt/app
 ---> 5765cdff9e66
Step 9/14 : COPY API/appsettings.json /opt/app/
 ---> b90aad29c756
Step 10/14 : COPY API/log4net.config.xml /opt/app/
failed to export image: failed to create image: failed to get layer sha256:8306960c4c2756916ec2882881527b6254b3a08ff467e0c68ab478cdac688125: layer does not exist

Describe the results you expected:
Successfully built image.

Additional information you deem important (e.g. issue happens only occasionally):

By re-arranging the instructions in the Dockerfile I was able to get this to build successfully:

FROM microsoft/aspnetcore:2.0

RUN apt-get update \
    && apt-get install -y nginx gettext-base python-pip \
    && pip install awscli \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

ENV LISTEN_PORT 80
ENV PROXY_TARGET_HOST 127.0.0.1
ENV PROXY_TARGET_PORT 5000

RUN mkdir -p /var/log/nginx && \
    ln -sf /dev/stdout /var/log/nginx/access.log && \
    ln -sf /dev/stdout /var/log/nginx/error.log

COPY etc/api.nginx.conf /etc/nginx/conf.d/mysite.template

COPY API/bin/Debug/netcoreapp2.0/publish /opt/app
COPY API/appsettings.json /opt/app/
CMD ["API.dll"]
COPY etc/run-site.sh /
RUN chmod +x /run-site.sh
COPY API/log4net.config.xml /opt/app/
ENTRYPOINT ["./run-site.sh"]

... which is obviously a bit of a mess towards the end. Not ideal.

Output of docker version:

Docker version 18.06.1-ce, build e68fc7a215d7133c34aa18e3b72b4a21fd0c6136

Output of docker info:

Containers: 3
 Running: 2
 Paused: 0
 Stopped: 1
Images: 42
Server Version: 18.06.1-ce
Storage Driver: devicemapper
 Pool Name: docker-docker--pool
 Pool Blocksize: 524.3kB
 Base Device Size: 10.74GB
 Backing Filesystem: ext4
 Udev Sync Supported: true
 Data Space Used: 11.06GB
 Data Space Total: 106.1GB
 Data Space Available: 95.02GB
 Metadata Space Used: 2.732MB
 Metadata Space Total: 109.1MB
 Metadata Space Available: 106.3MB
 Thin Pool Minimum Free Space: 10.61GB
 Deferred Removal Enabled: true
 Deferred Deletion Enabled: true
 Deferred Deleted Device Count: 0
 Library Version: 1.02.135-RHEL7 (2016-11-16)
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
 Volume: local
 Network: bridge host macvlan null overlay
 Log: awslogs fluentd gcplogs gelf journald json-file logentries splunk syslog
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Init Binary: docker-init
containerd version: 468a545b9edcd5932818eb9de8e72413e616e86e
runc version: 69663f0bd4b60df09991c08812a60108003fa340
init version: fec3683
Security Options:
 seccomp
  Profile: default
Kernel Version: 4.9.43-17.39.amzn1.x86_64
Operating System: Amazon Linux AMI 2018.03
OSType: linux
Architecture: x86_64
CPUs: 2
Total Memory: 3.86GiB
Name: ip-10-0-2-91
ID: CMMR:G5V7:7VMV:IFW5:NYLU:MJW7:4DDQ:DO3P:WASJ:BUN6:YCWI:DSQT
Docker Root Dir: /var/lib/docker
Debug Mode (client): false
Debug Mode (server): false
Registry: https://index.docker.io/v1/
Labels:
Experimental: false
Insecure Registries:
 127.0.0.0/8
Live Restore Enabled: false

Additional environment details (AWS, VirtualBox, physical, etc.):

This is an Amazon Linux AMI, one of the ECS-Optimised versions - amzn-ami-2017.03.g-amazon-ecs-optimized (ami-13f7226a). It has been updated with a full sudo yum update operation, including bringing Docker up to version 18.06-ce.