For me, I have 2 main problems I encounter over and over:

• not leveraging the framework currently in use, instead a lot of hacks are put together (usually involving global state etc...)
• writing functions of hundred or even thousand lines (not even kidding). Lack of separation of concerns is the biggest gripe I have.
• also, third one for the road (yes, I said 2 but I am on a roll): bad naming of things (functions, variables, everything...)

1. Lack of documentation: even comments in the code would be enough, but often there are not even that and to understand what a piece of code does, one must hope that at least the variables are sensibly named;
2. Libraries not updated because "It's just work in this way..."
3. Lack of configuration files: important variables, constant, url, server port, etc, inside the code (like spaghetti style) and not in a custom file to import or use.

I hate how things I did because I have found better ways to do it, but it's not possible to refactor everything all the time and sometimes the framework got optimised so it could have been done in a more optimal way, but again nobody wants to pay me to redo my work over and over.

Lack of organization in the API. When we were making the backend, we basically just created endpoints where we needed them, without bothering to have any organization of how we name them. Now the API is a bit confusing to work with.