The development team has been busy! 4.1.3 is now out and plenty of bugs fixed.

http://www.oracle.com/technetwork/developer-tools/datamodeler/overview/index.html

Bugs fixed (from the download pages):

22350565	String index out of bounds exception while importing structured type method bodies
22311829	Table report generating duplicate FK columns
22350611	Cannot select relationship/foreign key line
22339253	Change request report does not generate data in the report
22187312	Error when running design rules using Data Modeler version 4.1.2.895