Sam sometimes has a laser focus on a particular issue and loses sight of other things until they become quite large. Compensation is one example of that, another is hiring. The company, for quite a long time, has had a strong view on only hiring highly qualified, senior engineers. But without providing enough resources to shore up recruiting or providing top 10% salaries, hiring stagnated.
To make things worse, the work itself is actually not really all that challenging. It's a great place if you are a junior or mid-level engineer, but if you are senior or higher, you may find the engineering challenges boring.
The flat structure of the company also makes managerial opportunities limited. The previous requirement of "senior engineers only" meant that the existing engineers didn't have younger coworkers to mentor or technically challenging work to chew on. Everything is kind of a nice mediocre difficulty coming in at a unpredictable pace.
The office, while nice, was absolutely not designed for the size of the team. It was fine when the team was < 15 people. But having more than 30 people share two bathrooms is an absolute nightmare. The building itself also has terrible ventilation and can have +/- 10 degree shifts if you go from one corner of the building to another (you can feel it even if you walk the 100 ft from the front of the building to the back). In 70 degree weather, the area where the engineers sit can sometimes feel like it hits well over 80 degrees while upstairs and the front of the building is a reasonable temperature. 80 degrees with 20 sweating engineers also means it starts to smell.
The street ClassDojo is on is also a nightmare. Since it is an alleyway, all sorts of incredibly illicit and salacious activities occur on a daily basis. Pimps, drug dealers, public defecation, public sex, drug busts are just a few of the not-so-rare occurrences that happen in the tucked away corner of Tehama. But really, these kinds of things are common in the city of San Francisco, so it is hard to say of Tehama is any different.
All in all, the real problems facing ClassDojo are entirely solvable. The leadership is aware of them and is currently in the process of tackling them. The other issue, namely the office, is not entirely within the control of the company and more-or-less a larger societal ill. While ClassDojo is definitely well intentioned, this does not mean that they always get it right the first, second, or even third time. However, they do eventually get it right.