I've scored some of my best "hidden brown gems" in poorly kept LFS's, that be said, be extra cautious.
If you are worried, here's some thing you can do to help prevent a disaster
-Ask to see fish fed before buying
-Watch a potential new fish for a while, don't buy it on the first visit, check back a week later and see how it's doing.
-DIP EVERYTHING
-Take your time when inspecting corals before purchasing, never feel rushed into buying something
-Take any advise with a grain of salt, especially if it sounds a tad bit off.
-Use your smart phone to your advantage and look up anything you aren't sure about (maybe even negotiate a lower price)
Hope this helps, I've come across my fair share of spooky LFS's, but don't go in aggressive, always be courteous, even if you know some information may be a bit wacky!