When editing and pasting a procedure (in the database) I often; but surely not always get an alert - unfortunately I can't be more specific.
The alert tells me:
"Externally Modified Files"
"Procedure "my_procedure" has been modified outside Jdeveloper. Do you want to reload"
The procedure is not modified by any editors on my PC and surely not by anybody else.
Here is a recent discussion of the same topic, even though it is more discussion than resolution:
Modified by an external source
There was also a related bug, but only that the message identified the product as JDeveloper rather than SQL Developer ... however, I thought that was fixed.
SQL Developer Team