Salaries are flat out low relative to the talent levels and amount of equity given out doesn't fill the gap. The current weakness of the Australian dollar means jobs everywhere else in the world look appealing. Moving to Australia is a big draw but it is near impossible to get senior talent, especially from the US, to consider moving.
There are a lot of teams. Quite a few of them are not an ideal choice. Either because they're working on an also-ran product, because they're strategic priority #42, or because they're dealing with morass of cross-product work. For instance, you can work on billing systems at Atlassian...or thousands of other companies.
Some people and positions do not have good work-life balance. Often this comes from Team Leads or other more senior developers who put in long hours. Sometimes this is due to lack of training in delegation skills. Other times it is due to skill/expertise gaps. (When you grow this fast, you might be the only person on your team who has been around long enough to understand how that subsystem works.)
Quite a bit of silo-ification between products and geographies. That's somewhat understandable as the company has grown but it was a problem even when it was substantially smaller. This is a bit ironic given the tools that Atlassian makes.
I doubt this is unique to Atlassian but Product Management reigns supreme (over design and engineering). PMs are the ones who have meetings with the CEOs and GMs. There has been significant turnover among PM ranks and the general consensus is that the PM discipline has stagnated since a reorg from a functional structure a few years ago. The failure rate of new hire PMs is staggeringly high compared to any other role in the company.
Engineering and Product Development is a strength but many other functions have lots of room for improvement. HR is a perennial sore point for many. Lack of training and career progression have been a top complaint for years and very little has improved. Rollout of new systems (like applicant tracking systems) and processes takes just as long as at many other companies.
There's no two ways about it: legacy code. The main products are over a decade old. Atlassian has done an admirable job of maintaining high R&D investments (instead of turning them into cash cows with skeleton maintenance crews). But you'll be working on 13-year old Java download applications. The company is in the midst of an existential shift to find its way to a SAAS future but there's a huge gap between the products as they are today and how a product built from scratch would look.