Please tell me how did you configure the File Cleaner or did you used the default configuration?
There's an option under the second tab ("More") called "List all files from system Temp directories", I believe you had this option enabled. That would explain why those files were listed.
You can see the string which is used to identify unneeded files right from the product, it's under the "Unneeded files" box in the first tab of the File Cleaner.
With the current versions the settings are the following.
Safe mode: *.tmp; *.temp; *.gid; *.chk; *.~*;
Medium: Safe mode + *.old; *.fts; *.ftg; *.$$$; *.---; ~*.*; *.??$; *.___; *.~mp; *._mp; *.dmp; *.prv; CHKLIST.MS; *.$db; *.??~; *.db$; chklist.*; mscreate.dir;
Aggressive: Medium + *.wbk; *log.txt; *.err; *.log; *.sik; *.bak; *.ilk; *.aps; *.ncb; *.pch; *.?$?; *.?~?; *.^; *._dd; *._detmp; 0*.nch;