Many Pokémon have typings that don't have the most obvious explanations. If there are any Pokémon that have typings that don't make sense, post it here and let's try to explain it out. Let's start with and easy one that many people like to joke about. Charizard not being a Dragon typing.
Charizard is the original dragon image of Pokémon. And yet it has to be Fire/Flying... well at least they made it Fire/Dragon in its Mega X Form... Yeah? Why can't they be Poison or something? Like Grimer and Muk was...
Okay then. From what I can interpret, they had to do something for Charizard, with people saying it not being a Flying type also for have such giant wings. They could have possible made it a Fire/Dragon type if Pokémon abilities existed back then, and just to give it levitate. Also, it would be overpowered to give you one of the rarest and strongest Pokémon typings as a Starter, which would make the other two obsolete. For the Goomy line, it may be this way for it is likely based off a Sea Slug commonly refereed to as the "Blue Dragon Sea Slug".
I think you mean why isn't it a water type. It's not a water type because it just hides in the water because even a light flap of its wings can destroy a house.
For Scizor, it may be the reason of it evolving with the Metal Coat, and since it is based off of scissors.
I never understood Gyarados's water/flying typing. I suppose the 'flying' part could be a metaphor for a carp swimming up waterfalls to become a dragon, but I think that might be a bit of a stretch.