* In "Xmas Marks the Spot", the Ghostbusters trap the ghosts of Christmas Past, Present and Future all in one trap, and they all remain separate. But didn't another episode state that when you trap multiple ghosts in one trap, they end up permanently fused?
** That was "Drool, the Dog-faced Goblin." Um...okay, let's try to untangle this one. Drool and his Bigger Brother are "monster" ghosts; as such, they probably have low personal "integrities." That is to say, when locked in the trap, they fuse easily. The Christmas Ghosts, on the other hand, are personifications of Christmas, and their personal integrities are most likely pretty strong. Also, as revealed at the end of the episode, the Christmas Ghosts ''allowed'' themselves to be captured as part of their plan.
** This one has bothered me as well, especially in light of the fact that in the movie (the events of which are canon to the animated series) all the ghosts stuffed in the containment grid were able to separate after being trapped when the containment grid went nuclear (which is why we have Slimer running around), even though at one point in the film, foreshadowing the danger, Egon mentioned the super concentration of ectoplasm in the grid, implying compression. However, there is another possibility with the Ghosts of Christmas Past, Present, and Future. They may not be separate entities at all, but rather, all aspects of the same spirit. They wouldn't need to worry about separation, as they were already a connected entity to begin with.
** Several episodes are in contradiction with this. In "Ghosts ‘R’ Us" a family of ghosts is trapped together and later seem separated, even inside the Containment Unit.
** The episode that used the plot device "multiple ghosts sealed in one trap fuse together" was the (glaring and illogical) exception, not the rule.
** To be honest that sounded like an excuse from them to not release Drool. The only “explanation” I can think of for the discontinuity is that Drool was biting the other ghost at the moment of their capture which might be more invasive than be trapped together.
* In the climax of "Ragnarok and Roll," while the guys' plan to blow themselves and the villain up is noble and brave, how come none of them pointed out while agreeing to the plan that there were also two innocent bystanders on top of the building at the time? Yes, they had no choice, there were billions of lives at stake, they couldn't let that stop them, but still, it would've been nice if one of them had observed "But we'll take out the two of them, too" or told them to run for it (even though they probably would've refused).
** They had already pointed out that the explosion was going to take out several city blocks, and that there would be substantial collateral damage and civilian deaths, but that even wiping out lower Manhattan was better than the alternative. Presumably, the two bystanders on the building roof with them were included in that.
* Could someone tell me why the Ghostbusters had the Stay-Puft Marshmallow Man in the containment unit? This cartoon's supposed to have continuity with the movies, and the he wasn't trapped. He was blown up into marshmallow goo.
** The 2 prevalent fan theories are:
## It's another ghost, not Gozer, who took on that form, probably inspired by how an extremely powerful ghost took it on recently (supported by how his personality is nothing like Gozer's).
## The episode "Citizen Ghost" reveals that the Gozer-marshmallow-residue all over their uniforms was dangerous and needed to be disposed of (since Peter fails to do so, it turns into doppelgangers of the guys who nearly kill them). Thus, all the goo that rained down on NYC after the battle was just as dangerous, and the guys needed to dispose of it, too. How? By vacuuming it up and putting it in the Containment Unit, where it returned to its original form, albeit without the mind or personality of its maker (Gozer).

* So what are ghosts exactly? I mean are all of them spirits of the dead? I ask because then some episodes are really really very dark. One episode name “Baby Spooky” has a literal baby ghost walking around with her parents looking for her. The ghostbusters eventually help them reunite but, was he the soul of a dead baby? A family that died together? The episode itself sucks but that’s kind of a dark background if you think about.\\\
In another episode name “The Hole in the Wall” a house have ghosts like pests that come out of holes, depending on the size of the hole the size of the ghost. Alright, but then not only I find difficult to believe some of the small ghosts are spirits of the dead (one looks like a horseshoe with eyes) but also, what the hell is the big one at the end of the episode that is from the size of a Kaiju? And in general why some ghosts look like dead human (almost identical as how they were when alive but with some ghostly features like the zombies in Ray’s farm or Wyatt Earp) and other looks like something that Dali would paint during an acid trip?\\\
And what are the ghosts in Flip Side? Are all spirits of the dead that go there? Is that the afterlife? And if it is, then why do they have ghost versions of Peter, Egon and Ray, did they travel to the future when they died? (now that I think about that could explain Winston’s absent, he hasn’t die “yet” or he went to heaven maybe).
** The nature of the ghosts will vary from episode to episode. In some episodes yes, they are the spirit of the dead, most notably: the skeleton soldiers in "Bustman's Holiday", Ray’s farmer relatives in "Dairy Farm", the pirate ghosts in "Sea Fright", the ghost of Harry Houdini in "The Cabinet of Calamari", the one in "The Man Who Never Reached Home", Agatha Christie’s expy in Boo-Dunit and probably most of the ghosts in "Deadcon 1". Nevertheless other episodes made clear that other ghosts are actually creatures from AnotherDimension that were never humans to begin with like the aforementioned "Baby Spokens", “The Hole in the Wall”, “Trascendental Tourists” and probably the ghosts in “Flip Side” too, as some of the recurring villains like Samhain and The Ghostmaster. Slimer is most probably one of these cases. Other episodes have both like "Cry Uncle" have obviously the uncle who died and the more monstrous one to be one of these spirits. Other episodes like "Venkman's Ghost Repellers" with the New Jersey parallelogram and "You Can't Take It With You" show entrances to another dimensions where “ghosts” (as in weird things/life forms who float around) enter our world with no indication that they are human in any way or ever been.
** There's an alternate dimension home to supernatural, non-human entities. Some are spirits of dead humans (even animals); others are creatures originally from said alternate dimension. Since they apparently share many properties (ex. able to phase through walls on Earth and possess human beings), both types are collectively referred to as "ghosts." The Ghostbusters franchise may have been the first to use the term "ghosts" this way, but it hasn't been the last. Although a look at the classifications of different types of "ghosts" supposedly found in our world include more than just the spirits of dead humans, too...

* In the "Flip Side" episode, that is like a MirrorUniverse episode, why is Slimer's counterpart a monster? Shouldn't he be a human (just probably fat an evil) as everything is backwards?
** The Flip Side Slimmer makes sense in that it looks like an organic monster probably from another dimension. So, in a similar way how Slimmr is a good ghost living with organic beings (humans) the Mirror!Slimmer is an evil organic being living with ghosts.