Hi @Aaron PopeCongrats on the first post and welcome to BP, your life will never be the same:)This my best advice, and a common thread from experienced investors here on BP.

Sunken Master Bedrooms or Living Rooms are somewhat common, and shouldn't be a big issue.

Is this common practice, or do I need to find a new company to work with?

I'm going to guess that it is held as tenants in common - your husband and his sister. 

Just wondering with this vast number of people on this site if anyone has ever had this happen to them and is this really common?

You do see it in Boston, increasingly more every day, but that's the only place I've seen it commonly in this area.

It may not have a swimming pool and common amenities but good quality construction.  

That's fairly common.

I understand why Melanie is saying that you should work thru the listing agent to get a better deal - its a pretty common belief- but the reality is you shouldn’t get a better deal by working thru the listing agent, if anything you may not get the best deal possible because you aren’t represented.  

for me personally the only one I would trust to make a small business loan is my local commercial banker or credit union.even if they don't rip you off for advance fee's which is so common.. they never do end up funding.. business loans unless they are credit cards  are very tough to get.. if your getting a unsecured 500k business loanmeans you have at least 1 million in liquid cash and or securities..