PhD at the same university as master's
The most important part about where you do your PhD. is not so much about the standing of the university, but about the reputation of your PhD. adviser. Your name will be (forever) linked to his name and his reputation. If he is a well known researcher in your field, then you will carry this positive reputation with you. If he is not well known and he has issues getting funds, then in this case this might make your PhD. harder. If I were you, I would not worry about the reputation of University A., but about the reputation of your research group.

On another note, sometimes it can be problematic if you have done your Bachelor, Master and PhD. at the same institution. In this case, you will have experienced research in a single environment and this can be detrimental to your candidacy when applying for faculty position or etc. However, if you do a post-doc in another research group later on, you can mitigate this aspect. Like I said, if you feel the research group of University A has all you need and you like the work environment there (which is crucial to succeeding in your PhD.) then go ahead :)!.