Looking for examples of video games where the player is hypnotized. Cutscenes are interesting but I like when enemies can hypnotize the player if they’re not careful. Anyone have any examples?

Well, if you're looking for "character being hypnotized in battle", I think almost every rpg have some flavor of that.

For example Final Fantasy have the confusion state, berserk state and the charm state, Dragon quest too.

Breath of fire 3 have a command to guide confused/controlled/berserk characters to attack an specific enemy, the animation is a speech bubble saying "Yes sir".

Assassins Creed Syndicate has a side mission where the player (Jacob or Evie Frye) gets hypnotized to steal money for some top hat guy.

In Mass Effect 2 during Samara's loyalty side quest, you encounter her daughter Morinth. Basically an Alien succubus, if you don't select either the Paragon or Renegade speech options, Sheppard appears to begin falling under her sway.

For people who want to see this, here's a clip: youtube.com/watch?v=97DA44zDct8 from 50 seconds in to 1:20. I found it pretty hot, and I'm disappointed it gets interrupted.

But, there's more if you side with her character. She has the ability to both mind-control/seduce people into serving her and the ability to mind-meld with others and absorb their souls. She tries to tempt you into mindmelding, saying "My lovers spent their last moments experiencing pleasure you can't imagine. Like Nef--she died because her nervous system overloaded with an ecstasy so great she couldn't handle it. I want to give you that, Shephard. I want you to feel every nerve in your body pulsing with pleasure."

If you give in to her temptation, she does just that and kills you with the pleasure. It's definitely erotic. Here's a clip with female Shephard, 9:30 to end of video: youtube.com/watch?v=I_O1gdKzJoY
The same thing with male Shephard isn't as erotic, but here's the clip in case anyone would prefer malesub, 10:50 to end of video: youtube.com/watch?v=PMw4tKHndTY

There is also dragon quest. in fact in dragon quest XI there are several hypnotic enemies:

One is a cactus that makes party members laugh against their will

you have some cute female enemies who can charm supernaturally your party members

some very big muscled 4 armed cyclops can flex and use their hypnotic muscles (works even on male party members) which makes them fall in love with these big monsters and betray the party

some enemies can hypnotize the party to make them dance

Would you kindly remember what happens in Bioshock for me?

In Vampire the Masquerade: Bloodlines, if you refuse to do the Prince's quests early in the game, he will Dominate you into doing them anyway.

In Star Wars the Old Republic, the second act of the Imperial Agent storyline sees your character brainwashed with triggers used to control you. Freeing yourself from the conditioning makes up a lot of the Act's storyline.

Also in SWTOR, the Jedi Knight gets mind-controlled by the Emperor for a short period of time, though you get snapped out of it pretty quickly. I forget what act this happens in, as I only did the Jedi Knight storyline once.

Sometimes the protagonist, or some close to the protagonist, get hypnotized, BUT it's the bad/dead ending path.
Does it count for you?
Because in this case, in Fate Stay Night (the game of course), making the choice of letting Saber handle Caster give this kind of situation.
And there are other cases of course in other games.

Monster Girl Dreams features a number of enemies that will try to hypnotize the player during battle and one of the characters' story line involves turning you into her hypno-slave.

Do erotic games count ?
If that's part of what you're looking for, there's a loooot of them that have at least one enemy or cutscene somewhere where the main character gets hypnotized. (into sex most of the time)
Some even feature it pretty heavily, like Caliross, or BMOTV, for example.