During the past 10 years, there have been a handful of plot threads left unresolved from X-23's appearances. These can happen with any character for various reasons. It can be from a title being canceled, devices left for story potential to use later, and many more reasons than that.
In X-23's case, most stem from her mostly modern appearances. The v2 one shot, and v3 series both established new elements to her character that had yet to be fully explored. Her appearance in the Flash Thompson Venom event, "Circle of Four", has also presented some interesting material for exploration later. Those aren't all though. She has story aspects that can be explored as far back as even her origin.
The Telepathic Presence
This one comes from her v2 one shot and is carried over to her ongoing. Right before X-23 struck out on her own away from the X-Men, she picked up a little presence now that rests in her head. During the v2 one shot she's dealing with this "Game Master" picking apart of memories by someone trying to understand her, but doing it through rather odd means. We're never given a full explanation of who or what this presence is, though it shows up again during her v3 comic run as being caged by Beezle-Bub(the demon possessed Wolverine). After this event, the presence seems to have sunk back to staying quiet, but also may be working more cooperatively with Laura as well. With the addition of this story device, it covers a way to glance over memories of hers or even explain why some may be slightly not quite remembered right. This presence also gives her a means to potentially block out other telepaths as we saw with her blocking out Emma Frost early on in the v3 comic. His story has yet to be fully told other than he wants to rest and stop the constant noise he hears from the world. The only information available and the bulk of their interaction has been in the X-23 v2 Issue 1, the Women Of Marvel Oneshot special. We're also never told if her time at Avengers Arena or Avengers Academy interfered with how this being interacts with her. Avengers Academy itself having psionic dampeners. Avengers Arena itself is unknown though may have the same to deny the missing heroes from being found by telepaths.
Sigil of the Star Sword/X-23's Soul Mark
During the "Chaos Theory" arc we were given an explanation as to what this mark was from her earlier interactions with the demon Wolverine. It's a symbol that represents the Star Sword of the Enigma Force. What this means has yet to be fully explored.
Mr. Sinister's familiarity with Laura
During "Songs of the Orphan Child," we were given a glimpse into the fact Mr. Sinister knows Laura by name. This isn't completely surprising as he does keep tabs on all science related information across the board in the Marvel Universe, so he very well may have a file on Laura as he was one of the bidders in her earliest days. The question still remains on the familiarity of his tone by calling her Laura, a name she didn't receive until after escaping the Facility. He speaks to her like he may have an indirect tie from even after her Facility days, though none is ever spoken of. There are possibilities in this. He may have been one of the Facility staff albeit incognito and only to make sure their developments never could rival his. As mentioned, he was one of the bidders during her assassin for hire days. There's also the possibility that in Dr. Zander Rice's arrogance and attempts to outdo Laura's mother, that he used Facility ties to reach out to Mr. Sinister to help create Kimura's power set as well. This is another story detail that has yet to be explored and is unknown if ever will be. None of these explain the familiarity in his words by calling her by her first name. So far all we have been led to believe is that Ms. Sinister drew Laura in with misinformation. It did reveal other story potential though in the process.
X-23's Shifting Eye Color
Mostly this is considered a simple artist mistake, but during "Songs Of The Orphan Child" we're given a brief glimpse into the fact it may not be. During the issue itself, Laura's eyes shift colors from green to gray(X-23 v3 issue 5). She also notices similar from Alice and comments on it. Overall this has the potential to allude to there is more going on about this detail than what may be known as yet.
The Mystery Woman
She appeared twice in the X-23 v3 run without ever divulging her secrets. During Collision she premiered and showed us she has a mild familiarity with X-23 or at least her file. The inclusion of the original Triggerscent sample also seems to suggest some form of tie to the Facility which may explain the Mystery Woman's indirect involvement with Malcolm Colcord. After Kimura swore her vendetta and killed Facility Dr. Harkins during "Not Forgotten", she may have been replaced as a handler to track X-23. Is this mystery woman the Facility's new "retrieval expert?" Theories have ranged all over the board from her being a future X-23 gone bad, to potentially even a clone of her mother the Facility created in a bid to start trying to create a new ultimate weapon. The timing of her appearance after what was presented with "Songs of the Orphan Child" suggests she very well may be a clone of Laura's mother with limited memories or emotional blocks. It has also been mentioned that she is X-23's future, or represents her future. It's entirely unknown as in one regard she seemingly cares for Laura, but on the other end, she's not hesitant about putting Laura in danger. This could also be explained away though as she knows Laura well. This mystery woman knows that Laura can take care of herself. The more details analyzed, the deeper the mystery becomes with possibilities. As she's even presented ways to thank and help Laura along the way. Suggesting she is not entirely purely antagonistic towards X-23 as what would be expected from someone tied to the Facility.
The New Triggerscent
During the "Touching Darkness" story arc, we're shown the mystery woman had participated in creating a new Triggerscent. One that will work on normal people through bio-chemistry as opposed to the Pavlovian response Laura reacts to. This new weapon has seemingly gone into hiding, never being seen from again after the initial attempt of selling it. It does raise questions though over why did the mystery woman have this created, and to what ends does she mean to use it? She managed to get away and it is insinuated that she has reserves of this Triggerscent hidden away by how she prepared extra traps for Laura using it. Traps she knew Laura would overcome, and created what could be considered defining personal moments of growth and understanding.
During the Venom arc "Circle of Four," we're given a new story aspect to Laura's character. The debt token marker from the devil, as explored over in Venom, is a mark to suggest potentially a new leader of hell. With this marker comes a handful of potential new abilities that have only been explored on the already being able to shape shift Venom symbiote so far. How this marker may react with X-23, or mingle with the sigil of the star sword, is fully unknown. As far as we know, each marker may present its own set of properties or abilities per each entity it was given. There seems to be a wide array of surprises left with it as shown over in Venom. For example, Venom's marker was with the Symbiote. It was not with Thompson himself. The Symbiote had also found a way to transfer it through creating a new Symbiote from one it absorbed.
These are but a few of the outlying plot threads remaining from X-23's comic history. More to come soon when part 2 is complete as we dive into her stories from the past and present further!