Most of them are little things. Like a character I didn't plan to play a big role suddenly has a bigger role and my reasoning for said role had zero foreshadowing so it comes out of nowhere. Or I'm just not happy with a direction a character is going. Then I'll get some plot holes because I set something up to happen but it wound up getting abandoned. One issue I may wind up having in my Draygon books is how the two characters Siobhan and Wren are connected and why their magic reacts to each other so powerfully. I have vague ideas of how they're connected but until I get to that point where its revealed there is the very real possibility it falls flat.
I have written myself into corners but they haven't been anything that I couldn't idea bounce my way out of. Sometimes I'm not completely satisfied with my reasons but they still get me out of the corner. Best one I can think of right now in the Draygon books is I have a character Rosie who ran a place that basically amounts to a brothel. One of her serving girls wound up being the kidnapped cousin to another kingdoms ruler and so I on the fly had to come up with a reason why she couldn't remember being royalty. My bandaid fix was she had her mind wiped but it's a really stupid reason so I've made note that if I keep with that story line in future drafts I want to come up with something better. It still works in context, it's just a flat excuse imho.
Then in a book I don't have on Tapas, Power Uppers, I got almost the whole book written and realized the MC, Tayla, sucked. The secondary MC, Max, was a far better well rounded character. Tayla had things happen to her more than she made them happen. Where as Max had a well established back story, his reason for pushing against his fathers abuse of his sons super powers was a lot more compelling. I finished the book because it was already almost done by the time I realized how horrible Tayla was, but if I ever edit it's going to take a full rewrite and Max will become the MC. His story is just far more powerful.
I will fully admit that I sometimes have loose threads because of the way I write, but they're often minor things. But I don't feel like my first drafts have to be perfect and most of what I write will never make it to second draft for various reasons. If those loose threads are still there in a final draft I'm ready to publish and have people spend money on, then I have a whole other problem to my name. But in a first or even second draft it's simply not a big deal if I have issues I'm not satisfied with. There is a reason the saying is "writing is rewritting" anyone who thinks their first draft is perfect and has no mistakes is probably not being honest with themselves.