Wow....so many possible answers to your question. :-)
Anything that standing in the way of you getting all the information you need is always a warning sign.
On the seller side: A seller who won't allow a full inspection; won't provide information/documents you request; is not cooperative, etc.
On the property side: Issue with the neighborhood, vacant homes, comps much lower than your price, rents lower than those suggested by the seller, any issues in your home inspection, permit issues at the town hall, title issues, etc.
It really gets down to KNOWING your deal. Know what you are buying and know what it can rent/sell for and have multiple exit strategies (sell, rent, refi, etc.).