We walked from a house for less (bad roof that the owners didn’t have the cash to pay to fix). It’s why you do the inspection. As others noted, some of these things are things you now know to check when you see a house and are considering making an offer. When you view a house, by all means, flush the toilet, check to make sure there is hot water. Foundation issues are tough for us lay-folk to detect, but if there are a lot of little things that suggest poor upkeep, that’s the smoke that suggests a fire.
Assuming your loan was approved, you should be able to apply that same loan application fee to future purchases. Obviously some lenders or brokers vary in their policies, but most want your business enough to cut you some slack in cases like these.