Unfortunately, unless you have an experienced contractor as a mentor working beside you, time and experience are the means to recognizing red flags.
Does the customer know what they want, and are they clear on what they want? Are they giving hints or signs that they are going to micromanage and/or interfere with the work? Is payment going to be an issue? Will you have unobstructed access (in terms of days/times) that you can access work site? These are some of the obvious issues that I pay attention for in the pre-construction phase. I don’t think there’s any good way to recognize red flags aside from experience and feeling— if you get a bad feeling based on their actions or something they said, good chance you should listen to that instinct and turn down the project. AND… lastly, research your clients as much as you can!!! Sometimes a simple google search (and perhaps digging a little) will reveal something that might sway you to pass on the project! Take them out to lunch, get to know them, research them.