If you are getting this error consistently, there is a problem with the program.
If it were mine, I would do a series of compact operations. If that did not help I would look else where (Sorry I am not that technically up on deep problems within FTM)
One question: I could see an error occurring if the program loose contact with the exterior disk as it is closing the compact operation. Have you tried to see if the error occurs if you let the program pick the backup location, ie. folder "Family Tree Maker".
If this corrects the problem there may be a timing issue in the read/write routine of the computer, the external drive, and FTM. This is not fatal error just frustrating.
If it does not occur when you back up to the disk on which the program resides, you could then copy the backup to the other disk.
I back up to the folder created by FTM, "Family Tree Maker" containing the back up files, with the back up of the higher folder "My Documents".