Good advice all around from Paul T. and Munin. You two have explained the core PbtA philosophies well.

StormKnight, let me try and address your issues with MotW specifically. I've been running MotW for a stretch now, and it's a hack/setting that I really enjoy.

Moves
Manipulate Someone: Echoing the above, the key with this move is to start with the established fiction and go from there. If it seems like a monster/minion *should* be susceptible to the kinds of leverage hunters would apply (threats of violence... promised favors... flirtation, and so on), then let the hunters try and manipulate them! "Dream Away the Time" has notes on Oberon which make it clear that he's a minion who can be manipulated. If a hunter tries to manipulate a monster with no reasonable chance of coercion, don't call for the roll, and make sure the hunter knows this baddie isn't down for negotiations (always say what honesty demands).

Examples:
Ted, the Mundane: "Okay, so, what if I offer this vampire lord like, some blood? My blood? Will he go away then?"
GM: "'I need more than just one little snack,' he says." (offering an opportunity with a cost)
Ted: "How about... every month? My place?"
GM: "Roll manipulate someone."
Ted rolls and nails it at 10+. The vampire lord will skedaddle... for now.

Lane, the Chosen: "I tell the werewolf we'll buy it steaks if it stops killing people at the clown college."
GM: "It 100% doesn't understand you, and now it's advancing, baring some scary-sharp fangs. What do you do?"

It's also worth noting that the Monstrous playbook has as an advancement (Dark Negotiator) which allows a hunter to just generally manipulate monsters. I'd play that pretty loose--in the example above, maybe a Monstrous with Dark Negotiator *could* convince that werewolf with a nice ribeye.

Investigate a Mystery:
The questions given for this move (or for most PbtA-style "query" moves) seem more limiting than they actually are. I find that most of the time a hunter's investigate question falls into one of these categories, even if they're not asking that question word for word. Again, always look to the fiction and keep your answers grounded in the fiction as well. Don't answer a "What sort of creature is it?" by saying "It's a chimera made of household pets." Instead, give tangible details about the clues the hunters find.

Also, keep in mind that "What sort of" =/= "What is." Ghouls and carrion worms are both necrophages, and the hunters may need to do more investigating to suss out just what kind of corpse-eater they're dealing with.

Example:
Louisa, the Expert: "I'm scoping out the crime scene with my full toolkit out."
GM: "Give me investigate a mystery.
She rolls a 10+, meaning three questions.
Louisa: "What sort of creature is it?"
GM: "You have a ruler and magnifying glass, right? You measure some of the tracks--they're pretty deep, and spaced apart too wide for a regular wolf. You also find some long, gross hairs. This thing is some sort of bipedal animal."
Louisa: "Like a werewolf?"
GM: *coy glance* "You've got two more."
Louisa: "Okay. Does it have a den nearby, maybe?"
GM: "You're not sure about a warren but you see the tracks head north, through some thick brush, towards the park." (The GM didn't say it, but they're treating this as "Where did it go?" It's not a direct answer to Louisa, but it's not a lie, and it's in the spirit of her question.)
Louisa: "Yikes. I go over to the corpse and check him out. Like, what exactly happened?"
GM: "You said you had a year of pre-med, right? This dude's throat's been torn out--bite radius is *huge*--and, wow, it sure looks like something just tore his arms clean off." (You could count this as either "What happened here?" or "What can it do?," as we've established the creature is a biter and crazy strong. Answer's the same either way, and--again--it's playing fair with Louisa's fictional positioning.)

Read a Bad Situation:
The two most common uses I see are when the hunters are looking to setup an advantage in a fight, or when the hunters have walked into danger, but they don't know it yet. In the former, a hunter might say they're frantically looking around for something that might drive the giant spider away. In the latter, the hunters might have walked into the giant spider's lair, and the spider's hiding somewhere, waiting to pounce.

Examples:
Zuzu, the Divine: "This thing's killing us! Is there anything in the room that might help?"
GM: "Roll me read a bad sitch."
She gets a soft hit, so one hold which she spends asking for a way to "protect the victims."
GM: "There's one of those big red factory push buttons here which looks like it's connected to the loading gate. If you close that the spider won't be able to reach the bystanders on the other side."

The hunters have broken into a factory after dark, looking for the giant spider queen.
GM: "There's webbing all over the place. Blood, too. Man, this place looks dangerous! Anyone want to try and read a bad situation?
Zuzu: "The situation's bad?"
GM: "Zuzu, as you're walking along you accidentally kick a dismembered arm."
Zuzu: "I'M READING A BAD SITUATION."
She nails the roll and starts spending hold.
Zuzu: "Are there any dangers we haven't noticed?"
GM: "Zuzu, after kicking the arm you slowly look up, and see the spider queen hanging off the roof, high above you. It looks like it's ready to pounce!"

Kick Some Ass:
If your hunters are engaging in tit-for-tat scrums with monsters too often, consider a few things.

1) How tough are your big-bad monsters? Specific playbooks can get pretty tanky, but a straight-up fight with a vampire leader should never be a sure thing.

2) Are you using the harm moves? Even 0-harm exchanges can knock away weapons or put hunters in dangerous situations. (For example: one mystery I ran, set in a cannery, saw the hunters getting repeatedly knocked into the canning machinery by devious government reptilians.)

3) Are your monsters/minions too willing to "just attack"? You don't need to answer every kick assb roll with a strike of your own. Monsters can try to escape, try to hide in the shadows, try to do a maniacal monologue, and so on. A "trickster" monster might not even fight at all, instead opting to dance and dodge around, taunting the hunters.

Use Magic:
Should every hunter be able to use magic? In short: yes. In not-so-short: depends. As always, the fiction's the thing to focus on. Use Magic isn't an ability that everyone "gets"--it's a set of options, for everyone, guiding what *could* happen when someone in the fiction uses magic.

The better question to ask when this comes up (remember your principles: "ask questions and build on the answers") is "How do you do that?"

Examples
Ezekiel the Lesser, Spell-Slinger: "I'm going to use magic to place a binding spell on this clockwork tiger."
GM: "Okay, how do you do that? Like, where does this spell come from?"
Ezekiel: "Well, I'm a Spell-Slinger, so I learned it from my order during my training. It's an incantation, and I have to wave my hands like this." Ezekiel demonstrates.
GM: "Fair enough! Roll it! But, I'm going to say you need your spellbook to cast as well."

Morton, the Mundane: "I'm going to use magic to locate the missing children."
GM: "Woah, really? Aren't you a plumber Mort? Where'd you learn to do arcane geo-positioning?"
Morton: "Ah... I got nothing. I guess I'm calling my plumber buddies instead to see if they've seen anything on the job."

Now, there's nothing to say that Morton couldn't, eventually, learn some sort of basic magic. He's rolling with a crew of monster hunters, after all--maybe Ezekiel teaches him something! Point is, a Mundane or Professional (depending on the Professional's agency) aren't going to have as many good explanations for a use magic roll as, say, a Spooky, Monstrous, Expert or Spell-Slinger.

Motivations
These are chiefly for you, the Keeper. Isn't that nice? They're like the elevator pitch for that location/character. If you use them "incorrectly," your hunters will never know. That said, they *are* a good tool to have in your kit. When the hunters finally drag themselves over to the Sacrifice Pit, I'm not going to be scrambling through my notes, wondering what the hell I put that Pit in for. I just scan my locations for "Sacrifice Pit: Location: Hellgate," and I quickly remember that, oh yeah, that's where the stone golems are coming from.

It's the same for bystanders. While I might prepare a quick bio for each my key NPCs, something like "Dave Henton: Bystander: Detective" does *alot* of work when I need to pull Dave and his confounding inquisitiveness out in the middle of a mystery.

Let me know if this helps StormKnight. MotW is one of my favorites for quick n' easy RPG sessions, and it'd be awesome to hear that you're getting a better handle on the system.