There are three possible explanations:
a) you have a high traffic app and as you were making edits directly to the sheet, some updates from the app overwrite them — if so, then the solution is to Pause the app (Manage -> Deploy pane) when you are making direct edits
b) the direct edits are successful but then some time later, an update from the app overwrites them. This is by design.
The “last writer wins”.
c) you are adding new rows directly but also adding new rows via the app. In this case, check to see that your key column is chosen well (and not the _RowNumber). If there is a conflict between keys, then one could overwrite the other