Question
Why did FME not clean up the temp files it created during my translation?
Answer
If FME does not shut down cleanly the temporary files will not be cleaned up. A "clean" shutdown is when a translation is stopped by the user using the appropriate "Stop Translation" on the toolbar or when the workspace runs to completion on it's own. Examples of "unclean" shutdowns are when FME crashes, or if the Workbench was closed by the user in mid-translation.
FME can create quite large temporary files. If you suspect that there are temporary files use Tools>Purge Temporary Files.
You might want to consider changing the location of the FME temp directory by setting the FME_TEMP directory.