Atlassian's antics with Jira, Confluence, and BitBucket have really started to make me mad.
Jira is changing it's editor... slowly. The old editor had nice shortcuts, like h1. - h6., {code}, {blockquote} etc. When you create a ticket - it's the old editor, but when you edit a ticket or write a comment, it's the new editor! This new editor has none of the markdown-ish shortcuts the old editor had.
Confluence is also changing it's editor and the old wiki pages do not have a 1:1 match to the new wiki pages. This means you have to go through each page, convert it, and edit it to fix the broken things - because depending on what you use, it will be broken. For example, there is no longer a note, warning, or error macro - instead it gets turned into a info macro that you have to go in and edit it to the style you previously had. Code blocks no longer let you pick the color scheme you had, instead they're all generic. There's even more here I'm not listing.
Confluence has also just been wonky lately. It's supposed to automatically format a link into something nice (e.g. https://confluence/page-name -> Page Name or https://jira/AAA-1234 -> AAA->1234) and this only happens sometimes. Other times I'm finding the page frozen or slow and the only thing that fixes it is refreshing the page or publishing the page and going back to edit it.
Of course with BitBucket I dislike that they're dropping Mercurial. I understand why, but I am really going to miss it. Git is way more powerful but Mercurial is (at least to me) way easier to use and pick up. The infuriating part is that they offer no tool for converting existing repositories whatsoever. Github has a tool that will turn your BitBucket Mercurial repo into a Github repo!
For any tool that aims to be an alternative to Jira / Confluence / BitBucket, please don't do what Atlassian does. If you are going to make any transitions or any major change - please make it as easy and seamless as possible for your users.