1) Echoing many other reviews, the biggest con is the lack of work/life balance. The company is growing as such an astounding rate that it simply can't hire fast enough, and not for lack of want or effort. That said, the hours are long and the demands are very high, sometimes downright unreasonable.
2) In keeping with the above, compensation is far too low for the hours required. When hours and salary are broken down into practical terms, the hourly rate for work is inadequate, especially given the complexity and time urgency of the work.
3) Internal competition can make it too intimidating to use the "unlimited" paid time off that the company offers. Also, because the company is perpetually understaffed, taking time off can be impossible; frequently, employees have to answer emails, etc. while "off."
4) Managers have a tendency to railroad employees into reporting greater satisfaction than would be genuine. There is an overarching culture of pressure to remain cheerful and avoid dissent. Although they do use anonymous surveys, this is somewhat undermined by weekly face-to-face sync-ups.
5) The social element of the company is pretty lacking (or at least it used to be).
6) The CEO showed far more interest in the software team than in the operations team, even on a personal level. While I understand it is engineering and software that set Flexport apart from its competitors, it's important to remember that, without the tireless grunt work of the operations staff, the engineers would have no demand for their innovations.