Many people are very bad at raising concerns with their bosses and colleagues, and this causes a lot of unnecessary pain and suffering. If you want to get what you want, you need to get good at raising concerns in a productive and effective way.
1) Talk about interests, not positions. Classic example: two people sitting in a room. One says "I want the window open," the other says "I want the window closed." These are both positions, and they're mutually incompatible positions, so they can't both have what they want. Instead, the people should talk about their interests: one of them might say "I'm hot, one solution is to open the window," the other might say "there's a bad smell outside, that’s why I want the window closed." These interests are not mutually incompatible, so now the two people can come up with solutions e.g. turning on a fan, or opening a window in another room.
2) First try to understand why something is currently the way it is, before you try to change it. See also Chesterton's fence. Sometimes things are happening for bad reasons, sometimes for outdated reasons, but unless you know why something is happening then you might make things worse when you try to change it. Instead of saying "we shouldn't be doing X" or "X is stupid", come in by asking "is there a specific reason why are we currently doing X?"
3) Situate your listener: they don’t yet know what you know. Before coming to someone with a problem, go over in your head what the other person would need to know to understand that problem and ask yourself whether they already have that context. Check in with the other person while explaining the problem to make sure you're not giving either too much or too little detail.
Then, give the main topic up front. E.g. don't say "I have a problem: it started last tuesday when I went to the doctor and I was late for the bus and....", the listener will have no idea what they're meant to be listening out for or focussing on. Say "I have a problem with completing my project for next week, because...."
4) Assume good intentions as much as possible. Don't assume other people know your problems. Basically, everyone in life is super busy and dealing with a lot of different stuff and half the time they don't even know about your Huge Obvious Problem until you explicitly tell them about it. So most of the time you'll get further by assuming the other person wants to help you than by coming in confrontationally. (Usually).
If you want to go deeper on the negotiation side of things, read this online summary of the book Getting To Yes.