Hi. I've been trying Ugene for a couple of weeks and I'm impressed. Really nice program.
I found some possible bugs:

1 . Ugene crashes If I add new annotations to a sequence and then try to save a genbank file including annotations. Just create a New document from text, save it as fasta or gb and try to export after adding any annotation.

2 . It crashes If I create a document and then I try to change the name of the object (even if saving the file immediately is checked). No problem after re-opening the file.

3 . Just by chance found that in an alignment if I select a region with too many gaps (or only gaps) and try to re-align that region with muscle it crashes.
Note: after copying a region from an alignment, it brings the sequence and a trailing space that for example, bothers with the find function.

Please, let me know if you need more details.

Thanks.

(Windows 7 64 bits, Versión      6.1.7600, AMD Turion 64 X2 Mobile Technology TL-60, 2000 Mhz, Ugene 1.7.2)