Not sure if this will be a one-off, or an irregular thing; it depends on how many of the following come to mind.

How do we reconcile different stories that seem to contradict one another? That's something handbooks often have to do. Sometimes this is caused by one writer not knowing (or sometimes not caring) what another has already established. Other times it's because a retcon raises some queries about what we saw in other stories. The title of this thread comes from the most glaring example of this - Character A dies in a story. Character A is subsequently seen in the afterlife (Heaven, Hell, some spectral limbo) or as a ghost, so they are definitely dead. Character A is later revealed to be alive, and crucially, to have never actually died in the first place. So who or what did we see in the afterlife?

Sometimes there's an explanation readily available - Mockingbird was seen in the afterlife several times, yet turned out to never be dead. However, we also know she was impersonated by a Skrull, and that's who died. So it was presumably the Skrull we've seen in the afterlife. They were programmed so well to believe they were Mockingbird in order to go deep undercover that they continued to believe this after they died (or they are seeking redemption - being dead and knowing there (a) is a Heaven and (b) you didn't get in, might make you re-evaluate your past misdeeds). 

Other times we might be able to explain it by assuming the spirit we saw was another person who had used that identity. This can work when we know of multiple characters who wore the costume, more than one is dead, and the ghost never identified themselves by their civilian identity. 

It's also worth noting that clones can have their own souls, so any character who has ever been cloned can be both alive and still have a lookalike dead counterpart. We got this confirmed when several versions of Multiple Man turned up in Dead X-Men during the Chaos War storyline. Main body Madrox was still alive at the time, but we'd seen several of his clones die. Interestingly, though iirc they were eventually all drawn wearing the same outfit, the original plan was to have them in different outfits; the handbook team was asked to provide examples of Madrox clones being killed in past comics, so that the Madrox clones in Dead X-Men could be drawn wearing differing costumes that would clue informed readers as to which ones they were - e.g. one would be the clone whose body was stolen by Proteus, another would be the one who died from the Legacy virus, etc. 

But even when the above options aren't available, there's an established concept that is effectively a "get out of jail free" for explaining seeing a character's soul in the afterlife when the character was never dead. The second issue of the Marvel UK title Hell's Angel (later Dark Angel) revealed that souls can become fragmented by trauma, scattering them into pieces across various afterlifes (and other places presumably), with each fragment nonetheless looking whole to a casual observer and being able to act independent of the remaining fragments (think what happened to Arisen Tyrk when he was split into multiple Lunatiks). Though the character who explains the concept seems to believe this only happens when someone dies, it's not a stretch to suggest that near death trauma can do the same, meaning a souls fragment can exist for living people. 

Interestingly, one of the soul fragments in this issue is the Jordan Stryke Viper, then dead at the hands of Madame Hydra so she could steal his name, but who has since been seen alive and well without explanation for how he might have been resurrected. It's thus entirely possible that he never actually died, and the soul fragment in the Hell's Angel story was the bit broken off by the trauma of being shot and nearly killed by Madame Hydra.