I forget to start/stop the timer all the time, so I have run into this problem a few times since the version 4.0 update on March 2. While we're waiting for a fix, there are a couple workarounds.
Forgot to stop the timer
Problem:
Changing the Session Stop Time or Duration results in an error. (I believe this is caused by a rounding error, or similar, where the Session Start Time appears to be one second earlier than the Entry Start Time.)
Workaround:
1a. Set the Session Start Time one minute forward.
1b. Alternatively, you can set the Entry Start Time one minute backward using the workaround below.
Forgot to start the timer
Problem:
Changing the Session Start Time backward seems impossible.
Workaround:
1. Cancel the change to the Session and exit back to the Time Entry.
2. Set the Entry Start Time backward to the time you want, then tap Save to commit the change.
3. Go to the Session and set the Session Start Time to the same time. If that doesn't work, then set it one minute forward.
Edit: Oops, I just noticed Adam's link above, in which he says basically the same thing.