You did something bad. If I say, It'd be better if you didn't do that. <- this doesn't make sense in that context, as it refers to the future. I wish you hadn't done it. <- That's fine. You just came in. If I say, It'd be better if you didn't come here. <- Again, that is future, so isn't appropriate. I wish you hadn't come here. <- that's fine.

There are subtle differences. You did something bad. Option 1: "It'd be better/best if you didn't do that." Stop doing that. Context: It'd be better/best if you didn't interrupt the director when he is in a meeting. If you do it again, you might get in trouble. Option 2: "I wish you hadn't done that." (not "it," but "that") I am personally affected by what you did. Context: You shouldn't have interrupted the director when he was in a meeting. I am worried that he will wonder why I hired you. Option 3: "You shouldn't have done that." You may already be in trouble. Context: You shouldn't have interrupted the director when he was in a meeting. He'll probably come over and yell at you once the meeting is over. He did that to me during my first week on the job. You just came in (or came here). "It'd be better/best if you didn't come in/come here." (please don't do it again) "I wish you hadn't come in/come here." (maybe because I didn't want to see you today) "You shouldn't have come in/come here." (maybe you were not invited/you are not allowed/it is dangerous here) I hope that helps.