Well, for the conflict of schedules, in my environment, you are encouraged to plan your own academic development. So if you decide you'd rather do A then B, as long as it fits within the framework, you are allowed to do it.

The second one, you can't be there because you have to work? Isn't your PhD your job? Slightly confused about that. I think it is natural that your PhD comes first. I feel like the correct path would be to be there, but to attend your supervisor that she/he should give you an earlier notice next time, to prevent conflicting schedules.

Like Lonely Warrior mentioned, you don't say anything about how you communicate with your supervisor. Is that going ok? Because that's crucial.