Is time to deliver data included in time measured for a Slow Query
It is absolutely possible the application taking a long time can cause those numbers. From the slow query manual (emphasis mine):


  mysqld writes a statement to the slow query log after it has been executed and after all locks have been released


So if your application is taking a long time to release any lock that it acquired for the session, the query time written will reflect that.

Now in your specific scenario, is it possible that the slow execution times are occurring during some heavy load on your database server? That would cause abnormal query times irregardless of slow lock release.