My boyfriend's sister does not like me anymore

We where really close at first. My boyfriend and i are pretty serious now, and we have been dating for two years. Recently thought his life got very complicated with school and his job and it stressed him out so much. His stress caused us to fight, a lot. But now things are much better now, and my boyfriend and i are very happy.

Well one day my boyfriend came home late from a friends party, around 2am. He called me to let me know he was ok. He also told me that if the phone cut off, that i should call him back. (His phone was broken, and it was acting funny, so it cuts off sometimes) Sure enough the phone cut off, so i called him back. There was no answer, so i just went to sleep.

A few days later, his older sister messages me on Facebook, and told me that i need to back off from her little brother, because i was calling him late in the night, and i was waking up their mother from sleeping. I thought this was a little strange, because his sister lives way out of state with her husband, far from me and my boyfriend, and his mother. Which means that my boyfriend's mother must have told her daughter about it over the phone or computer.

Anyways, i told his sister i was sorry, and we have not talked since then, which was three months ago. Well ever since i told my boyfriend what his sister told me, he has been keeping our relationship kind of a secret. If we talk late at night, he makes sure his sister and his mom do not know about it, it kinda hurts me, because i never meant for any of this to happen! If only i had just not called back that night.

what do i do? Should my boyfriend have stood up for me? Is it right for him to be keeping it a secret from them? I feel like he wants his sister to think he does everything she wants him to, but in secret he does what he wants to do. It really hurts me to think about this, because it makes me think one day his sister is going to break us up.

Thank you guys for reading all this
~Kay