I ran 2.9 for awhile and didn't have any problems, but that's just me. Moodle 3.0 was a little different, always fixing bugs along the way. All software has bugs. What I have found with my rather simple Moodle installation is that upgrading is safe. However, it is always wise to upgrade an experimental version of your moodle before upgrading your production moodle. For example, 3.2 was a more significant upgrade and took me awhile to explore it (on my experimental server) before upgrading my production moodle. 3.2 brought to us a new base theme too.
Some of these upgrading issues will also depend upon how much customization you have done to your moodle.