BACS.IP relies on the underlying Operating System to inform it that a new file has been created. These notifications can be erratic and sometimes Windows reports that there are two new files in a directory when there is actually only one file.
The file is successfully imported, but then the software tries to import a file which doesn't exist (since the file which was detected would already have been imported and moved).
To avoid this, against the appropriate Back Office profile(s) select the 'Poll directory' option. This changes the behaviour of BACS.IP so that it does not rely on the Operating System to notify it that a new file has been created. Instead, it checks the folder every 30 seconds and imports any files it finds.