Processes, processes, and processes. Whether it's the mandatory 4 course training on network security alone, or the process to merge code into the release branch, or the processes to transition a story from development to ready to release, the company is obsessed with having many processes in place, which usually bogs down engineering velocity and work quality. There were also many rules that dictated how employees should behave outside of work, such as discouragement of working in for profit gigs outside of work, or having appropriate LinkedIn profiles, these I found too intrusive.
Lack of Transparent Performance review. The upper management decides the grading, and there is a lack of transparency at the engineer level.
Low pay. Some engineers are severely underpaid.
Lack of cross functional team collaboration. Whether it's engineers in other teams or non engineers, collaboration is lacking and people are not grateful that engineers are there to help or are not patient when they are helping you.