The reason that it appears with some, but not others, is that on the "good Clips," you have adequate Handles, and on the "bad Clips," you do not. It is about the In & Out points.
PS - Besides the info in the Help File, see this ARTICLE (much from various Adobe Help Files).
Think about it this way: you can't tie a knot with just the ends of two pieces of rope. You need some overlap. The same applies to transitions; you need overlapping material--commonly called handles--to create a transition. If you don't have enough material as required by the duration of the transition, you'll get that warning.