I found that this was a problem for me because I was compiling my source files without line numbers. If this is your problem, you will see
[cobertura-instrument] WARN visitEnd, No line number information found for class com.x.y.z.A.
Perhaps you need to compile with debug=true?
To solve this, add debug="true" debuglevel="vars,lines,source"
to your javac
command.
See also:
http://meera-subbarao.blogspot.co.uk/2008/07/cobertura-instrument-warn-visitend-no.html