This is intermittent I'm afraid, but quite regularly when I copy a file by 
right clicking on a source file in the project tree view and selecting copy, 
and then paste by right clicking on the parent package and selecting paste I 
end up with two copies of the file.

Correct operation=
Copy Test.java
End up with Test.java and Test_1.java

But sometimes I get=
Copy Test.java
End up with Test_1.java and Test_2.java

If I keep deleting Test_1.java or Test_1.java and Test_2.java and keep pasting 
the file then sometimes I get just Test_1.java and sometimes I get both!