* UPDATE *
I figured the best way to run some commands is to write a custom Dockerfile that does everything I want before the official CMD is ran from the image.
docker-compose.yaml:
version: '3'
# Can be used as an alternative to VBox/Vagrant
services:
  mongo:
    container_name: mongo
    image: mongo
    build:
      context: .
      dockerfile: deploy/local/Dockerfile.mongo
    ports:
      - "27017:27017"
    volumes:
      - ../.data/mongodb:/data/db
Dockerfile.mongo:
FROM mongo:3.2.12
RUN mkdir -p /fixtures
COPY ./fixtures /fixtures
RUN (mongod --fork --syslog && \
     mongoimport --db wcm-local --collection clients --file /fixtures/clients.json && \
     mongoimport --db wcm-local --collection configs --file /fixtures/configs.json && \
     mongoimport --db wcm-local --collection content --file /fixtures/content.json && \
     mongoimport --db wcm-local --collection licenses --file /fixtures/licenses.json && \
     mongoimport --db wcm-local --collection lists --file /fixtures/lists.json && \
     mongoimport --db wcm-local --collection properties --file /fixtures/properties.json && \
     mongoimport --db wcm-local --collection videos --file /fixtures/videos.json)
This is probably the cleanest way to do it.
* OLD WAY *
I created a shell script with my commands. In this case I wanted to start mongod, and run mongoimport but calling mongod blocks you from running the rest. 
docker-compose.yaml:
version: '3'
services:
  mongo:
    container_name: mongo
    image: mongo:3.2.12
    ports:
      - "27017:27017"
    volumes:
      - ./fixtures:/fixtures
      - ./deploy:/deploy
      - ../.data/mongodb:/data/db
    command: sh /deploy/local/start_mongod.sh
start_mongod.sh:
mongod --fork --syslog && \
mongoimport --db wcm-local --collection clients --file /fixtures/clients.json && \
mongoimport --db wcm-local --collection configs --file /fixtures/configs.json && \
mongoimport --db wcm-local --collection content --file /fixtures/content.json && \
mongoimport --db wcm-local --collection licenses --file /fixtures/licenses.json && \
mongoimport --db wcm-local --collection lists --file /fixtures/lists.json && \
mongoimport --db wcm-local --collection properties --file /fixtures/properties.json && \
mongoimport --db wcm-local --collection videos --file /fixtures/videos.json && \
pkill -f mongod && \
sleep 2 && \
mongod
So this forks mongo, does monogimport and then kills the forked mongo which is detached, and starts it up again without detaching. Not sure if there is a way to attach to a forked process but this does work.
NOTE: If you strictly want to load some initial db data this is the way to do it:
mongo_import.sh
#!/bin/bash
# Import from fixtures
# Used in build and docker-compose mongo (different dirs)
DIRECTORY=../deploy/local/mongo_fixtures
if [[ -d "/fixtures" ]]; then
    DIRECTORY=/fixtures
fi
echo ${DIRECTORY}
mongoimport --db wcm-local --collection clients --file ${DIRECTORY}/clients.json && \
mongoimport --db wcm-local --collection configs --file ${DIRECTORY}/configs.json && \
mongoimport --db wcm-local --collection content --file ${DIRECTORY}/content.json && \
mongoimport --db wcm-local --collection licenses --file ${DIRECTORY}/licenses.json && \
mongoimport --db wcm-local --collection lists --file ${DIRECTORY}/lists.json && \
mongoimport --db wcm-local --collection properties --file ${DIRECTORY}/properties.json && \
mongoimport --db wcm-local --collection videos --file ${DIRECTORY}/videos.json
mongo_fixtures/*.json files were created via mongoexport command.
docker-compose.yaml
version: '3'
services:
  mongo:
    container_name: mongo
    image: mongo:3.2.12
    ports:
      - "27017:27017"
    volumes:
      - mongo-data:/data/db:cached
      - ./deploy/local/mongo_fixtures:/fixtures
      - ./deploy/local/mongo_import.sh:/docker-entrypoint-initdb.d/mongo_import.sh
volumes:
  mongo-data:
    driver: local