Difference between mongod and mongodb upstart jobs
I suspect you had MongoDB 2.4 installed previously.

In MongoDB 2.4 the service was called mongodb and used /etc/mongodb.conf (ref: Install MongoDB 2.4 on Ubuntu).

With MongoDB 2.6 there was an attempt to have more standard package names across Linux distributions, so the service was renamed to mongod (to reflect the actual daemon being started) and the config was changed to mongod.conf (ref: Install MongoDB 2.6 on Ubuntu).