Other commenters have hit on this already, but the worst one that bites me all of the time is this one:

1. I click a link to an issue 2. I need to do something on that issue, so I attempt to click on a particular section to go make a modification 3. Bam, some background script has loaded, some new piece of content was shoved in, and what I clicked wasn't the thing I was expecting to click

Also, certain interactions within JIRA take far too many steps, and each one takes far too long to load, so it makes me dislike JIRA even more.

Project managers love JIRA, but engineers don't, because each time you make us wait we are less inclined to deal with the software that PM's need us to use so they know how things are going, so instead we get more meetings. If JIRA were fast, we could cut down on meetings.

Please make JIRA fast.