To be honest, in my opinion this is one is quite ambiguous, as it would likely depend on the context. Either suggestion for both statements could be accurate.
The construction of the first part of the statements as a little odd, as I would more likely go for "you came home early (...)" in most circumstances. Whether this is intentional or not I don't know. But with that wording, it would very much depend on context.
If "didn't come home late" is intentionally worded that way, while technically meaning the same thing, the use of the word didn't (in my opinion) suggests a negative connotation, so I would make a guess that it's more likely to mean that you didn't come early, despite your dad asking you to come home early.
On that one though, if the person making the statement isn't a native speaker and doesn't quite have a solid grasp of the language, and the tone of the sentence isn't clear from context, it could be either.
TL;DR: A and B imo mean 1, and C means 3, but in no way is it a straightforward answer.