I think a brief examination of the words "in" and "from" will help.
Though they each have myriad definitions and I am without an OED at work, for purposes of this discussion,
"missing" means unfound.
"in" refers to placement or location within.
"from" refers to source.
Note that in some cases they are interchangeable, at least in conversation. But their nuances are unmistakable. Unfortunately, not sure you'd be able to come up with a hard rule to follow, at least not a "when using -ing adjectives, use 'in'" type of rule.
If you're discussing being lost within something, you're indicating that placement or location is unknown. E.g., "Missing in action," "What's missing in your apartment?" You suppose that their existence is true, but that their temporal or spatial position is missing.
If you're attempting to convey that something is lost entirely from its source (or contested source), you'd use "missing from." E.g., "John was missing from the meeting," "His conclusion is missing from the paper." In these cases, their existence within the proposed scope is an unknown but likely false proposition. Its entire source, not its position, is missing.
Depending upon your philosophy and confidence in sensory perception, I suppose "missing in" could (almost) always be right. But "the answer is missing from the answer key," would be my preference if you are supposing that answer should or be found in a specific source (the answer key) but is not.
That's all I got. Hope it was clear, I'll update later if anything changes after I dive into resources at home. I'd specifically like to clarify the meaning of "from" in this case. "Source" or "scope" was the best I could come up with.