Just talk to him/her/it
My rule of thumb for romantic relationships and close friendships, for when the other person did something that bothers you and you’re wondering whether it’s worth bringing up. If you end up spending any non-trivial amount of time wondering whether to say anything, then that alone is already bothering you enough that it’s worth bringing up.
In my experience, such things are nearly always caused by misunderstandings or things that can be fixed trivially anyway, so this rule ends up eliminating long-term discomfort and improving communication for the cost of a small bit of short-term discomfort. If you’re worried about the other person’s reaction, it can help if you start by “this was almost too minor of an issue for me to bring up, but…”.
Most importantly, the rule is motivated by a desire for symmetry: if the other person was feeling bothered by some minor thing I did, would I want them to waste energy guessing whether or not to they have the courage to say anything to me? Of course not! And I can’t convincingly encourage them to speak up in such situations if I don’t show an example.
It often feels like staying quiet and accepting the discomfort would be making the other person a favor. But those small things that you didn’t feel were worth mentioning will start piling up and eating into the extent that you like your friend or partner. You’re not doing anyone any favors if you’re eroding your relationship because you don’t trust the other person to react reasonably to your feelings having been hurt.
(Disclaimer: This advice is calibrated for people with no serious self-esteem or mental health issues. There are situations when you actually can’t trust the other person to react reasonably. If you do want to stay close to them regardless, try to make sure that you also have other people with whom your relationship is more functional in this respect.
And of course there may be situations in which you know that you are being too sensitive and don’t want to bring up things because otherwise you’d be constantly expressing your unhappiness with something. Even in that case, though, it’s better for the other person to be aware of your sensitivity – if not every specific concern – so that they can help you overcome it. And knowing that you’re generally reluctant to express your concerns may make it easier for them to explicitly ensure that you’re alright with things that it would be reasonable to get upset about. Also, do make sure that it actually is you who is being too sensitive, rather than you being in a relationship where the other person doesn’t respect you and belittles your concerns.)