So, not all "WTF" moments are equal here, but:
-Army Men: Major Malfunction (that's right, kill the main character of the series off in the intro cutscene for no reason...yep...)
-Call of Duty: Infinite Warfare (something I don't understand is why the writers had the events take place all in the one day. Like, even if you didn't do any side missions, no soldier could do all these operations and live, either from exhaustion or lack of planning. Nothing about the plot requires that the events take place over 24 hours, and if anything, it weakens the intiial premise that the UNSA's main goal is to simply buy time for Earth to re-arm)
-Diablo Immortal (I'm not nearly as offput by this game as many are, but as far as I can tell, there's absolutely no reason to not port it to PC or console)
-Final Fantasy X (I enjoy cutscenes. I don't enjoy cutscenes when they're unskippable, and therefore, I have to see them every time I die after a boss. Jecht's final farewell to Tidus becomes less emotional when you're forced to see it again over...and over...and over...and over...and...)
-Golden Sun: Dark Dawn (like I said, not all WTF moments are equal, but, well, I'll put it this way. GS2 didn't need a sequel, but it did leave two potential hooks, namely Alex, and Anemos. Dark Dawn sidesteps the first, and ignores the second, to draw out new plot points that aren't fully resolved, and now, probably never will be)
-The Lord of the Rings: The Third Age (WTF was up with just skipping from the Peleanor Fields to the heroes being atop Barad-Dur confronting the Eye of Sauron? Did they run out of time?)
-Mass Effect 3 (the ending. I mean, how did they think the original ending would go down? I ask because the extended endings work so much better, I don't get why they weren't there from the start.)
-Mortal Kombat (so they rebooted the series, to reboot it again after the third game? Um, okay...)
-Perfect Dark Zero (the drastic shift in tone and aesthetic from the original. Don't get the choice.)
-Quake 2 (why is this Quake 2? I mean, I know why, but it's the start of an identity crisis for Quake that I'd argue it's never recovered from.)
-Resident Evil: Re:Verse (stop with the multiplayer crap Capcom. Just. Stop. Multiplayer RE is never going to be a thing. Or at least use Outbreak as a template rather than...whatever the hell this is.)
-Sonic the Hedgehog (2006): You could argue the whole game, but while that still had ambition behind it, Elise kissing Sonic...no. Just no.
-Star Fox Zero (said it before and I'll say it again, Nintendo has no idea what to do with Star Fox conceptually. It's why we get another reboot that adds nothing to the series in terms of story/setting, especially since Command had explicit sequel bait in a no. of its endings)
-Tomb Raider (I don't know why they're merging the Original and Survivour Timelines together.
-Warcraft III: Reforged (reportedly, the release was rushed by higher-ups, but I'm going to ask them, how the hell did they think it was going to go down? I mean, if they wanted to kill any chance of a WC3, well done, but aside from that?)
-Wing Commander: Prophecy (what the hell were they thinking killing off Blair like that?)