K., any bedroom (meaning the largest room)you're in is the masterbedroom. It isn't important that you have the biggest bedroom in the house, you just need your space. If you can fit your things in the room and you have access to each other, what does it matter?
Our "master bedroom" goes to our boys, there are four of them and only two of us, so it makes sense. We have two girls in one room, three girls in another, and our youngest is with us for now. It works just fine.
If it's down right seriously important for you to a room that's very large for whatever purpose, you can always knock out a wall to create that. And don't buy into the whole bit that you won't be able to sell your house if you don't have a master suite...there are many people who will buy it without...there's a house for anyone and someone for any house!
BUT, perhaps, it isn't the bedroom thing that's really giving you red flags about the house. If it's a perfect house but you just can't shake an odd fealing about it; don't get it! Listen to your intuition. Perhaps the neighbors are wacko and/or mean. Perhaps there's a flooding issue no one's mentioned...you know, trust yourself...even if you don't have a concrete explaination.