First off, as has been pointed out innumerable times, faking photos is easy especially now with all the digital doohickeys and whatzits. (Darkroom tricks can be done to accomplish the same end although I doubt much film is used these days.) It is to the point that photographic evidence is no longer reliable. This is made worse in the original event (UFO over New York) since there was only one witness. There was no corroborating testimony or evidence, photographic or otherwise.
There's also the convenience of how that UAP showed up the second time so Mr. Titus could get a photo of it. That's a little too convenient to fall within the realm of probability.
Getting back to generalities and discounting fakes, though, a very good one is misidentification of known objects. One I know about first hand is how the sun can hit an airliner in such a way that the only visible reflection is from the fuselage. That way a completely mundane airplane becomes a cigar-shaped UAP. Another is ball lightning. Another is weather inversions forming layers from which distant lights can reflect. And so on. And so on. And when they're exhausted, a sighting becomes an unknown in which case both sides are obliged to provide overwhelming evidence theirs is the right one. Thus far, no one has been able to in any case going. That's why they're still unknowns. However, unknown does not automatically equate to ET.
I'm very uncomfortable with the UFO over NY case in any event. Something's not right and I'm not going to speculate what right now; I have more critical things to think about. Further, having MUFON handle it won't do any good because they won't test all possibilities before declaring "Yes, by golly, we have a winner!" NICAP at it's top form would have been better but it's gone.