My guild recently noticed that one of our players, Ownsuall, pug run is showing up in our rankings. The odd thing is that he didn’t upload any logs to the guild page nor is there a listing for it. We wish for it to be removed, but are unable because it isn’t listed in the uploads. Please fix this if possible! Thanks!
Here are his rankings that are showing up: https://www.warcraftlogs.com/rankings/guild/257707/latest/
Sorry for the late reply, but no. He was the only one from the guild in the run as it was a personal pug run. Even then, the report isn’t in the guild upload so it shouldn’t be there. I’ve ran plenty of pug runs with guild members and uploaded to my personal logs. None of these showed up on the main guild page. On a side note, one of the logs went away on their own, but the other remains. He isn’t even in our guild anymore 
Ok I think there’s some confusion here. The guild rankings page is just a filter that shows all individual rankings earned by players that were in your guild at the time.
It sounds like you want a couple of features here if I am understanding correctly:
(1) A feature that excludes rankings that weren’t earned as part of a guild run. I can’t do this by default, since sometimes guilds get together to clear Normal/Heroic etc. with no clear majority, but those players still want to see themselves in their guild rankings lists. For example guild A and guild B have a 50/50 split in a Normal clear, but they’d still like to see their players show up in the guild rankings when they view them.
(2) “He isn’t even in our guild anymore” … sounds like you want to be able to limit the rankings shown only to current members. A reasonable request. Again, I can’t do this by default, since it’s important to preserve history. For example, if you go back and look at a guild’s rankings for Hellfire Citadel in Warlords of Draenor, you want to see rankings of people who were in your guild at the time and not limit yourself only to current members.
I do think there is room for some feature improvements here (basically for some additional filtering options), so I’ll add these suggestions to the feature queue.