Some that I feel are common. And some that I'm guilty of, myself:
-The person who took out the cameras on Egghead. This was most likely Van Augur. I'm still hoping for a SBS that clarifies this. But, I think most of the fanbase has probably moved on from this mystery.
-What the Celestial Dragon's "-Sei" and "-Gu" honorifics mean. The wiki makes it seem like it's already determined to be a male/female difference. But, personally, I think it's more likely to be a older/younger difference, myself. Either way, right now, it's treated like something that's already a known fact by most of the fandom.
https://worstgen.alwaysdata.net/forum/threads/celestial-dragon-honorifics.59163/
-Who Franky's father is. The Vivre Cards HEAVILY imply that it's Queen. But, technically it hasn't actually been revealed, yet.
-That Blackbeard is even capable of using a third Fruit. We all kind of assume he'll do this at some point, because of all the "3"s associated with him. But, technically, there's nothing in the story to say that he can.
-Shamrock being Bonney's father. This is the newest one. But, it does kind of make a twisted amount of sense.
-Tritoma being Boa's mom. It's just never been technically confirmed.
-That Momonosuke is the "controller" for the Ancient Weapon Pluton, the same way Shirahoshi is for Poseidon. I think most fans have assumed Momo has a connection to Pluton in the same way.
-That ALL Devil Fruits have some level of "will" of their own. This was really only explicitly stated to be a thing with Zoans. But, I think most fans kind of assume that Fruits like Ace's Flame Fruit contain a least a trace of Ace's will.
-Hibari being Akainu's daughter. Now, there is some proof of this, due to them both having the same accent and blood type. But, it's never been stated.
-The Red Line being a unnatural construct. Again, there's some proof to this, but it's treated mostly as a known fact in the fandom.
-If the Ancient Giants are the same thing as the "Oni". The way Kaido speaks, it sounds like they could be the same thing, but we just don't know for sure. And the difference is so minor, I think most fans kind of assume one is the same as the other. For good reason, mind.
-That the Gorosei don't have Devil Fruits, but instead have "Yokai" powers from Imu. Some people are treating this like a done deal, but we just don't know yet.
-That Robin was telling the truth about there being a "Age of Heaven" in the first place. So many big theories revolve around this being a real thing, when she was busy lying to Crocodile about what was on Alabasta's poneglyph.