I am running my python application in apache environment and using timedRotatingFileHandler to log. I have setup logger in a way that It is supposed to rotate midnight every
You can't log (and rotate) to the same file from multiple processes naively because OS wouldn't know how to serialize the write and rotate instructions from 2 different processes. What you are experiencing is known as a race condition as 2 processes are competing to write to the same file and close it and open with a new file handle at the same time at rotation time. Only 1 process will win a new file handle when you rotate, so that may explain the missing log event.
Here's a recipe from Python's documentation with hints about how to log to the same place.
http://docs.python.org/howto/logging-cookbook.html#logging-to-a-single-file-from-multiple-processes
Essentially you will want to have a separate process listening to logging events coming from multiple places and then that process will log the events to a single file. You can configure rotation in that listener process too.
If you are not sure how to write this, you can try using a package such as Sentry or Facebook's Scribe. I recommend Sentry because Scribe is not trivial to setup.