I'm not 100 percent sure, I've heard different things. You can see downvotes in memestream memes, like in
imgflip.com/m/templates or
imgflip.com/m/needameme but not on front (hot or latest) pages. The front pages used to look like memestream memes, but the web code for the front pages was updated over a year ago. On front page memes, only upvotes appear to get counted in the meme and comment up counts, downvotes don't hit those. Some users say they can see downvoting in the meme upvote count, I have not. On comments, downvoting can be inferred. If one top level comment shows 4 upvotes and is lower than a 3 upvote top level comment, I think that is an indication there was a downvote.
One thing I've noticed in my time here is my upvotes can take some time to affect the up count, usually milliseconds, sometimes a few minutes, once in a while up to 5-10 minutes, page refresh doesn't matter when looking at the meme up count. There is a tab on your profile page called "my likes" if you look at the meme upvote count there, it seems to always instantly reflect the true meme upvote count. I think that has to do with imgflip's architecture that relies on Amazon Web Services. Virtual databases running on virtual machines in the cloud.
As far as a complaint to the mods for this meme here, that is possible if there is copyright infringement maybe some other terms of service violation. I doubt that was the case here. Another more likely possibility that just occurred to me is a site glitch. I have seen about 5 or 6 of those in my time here. I can go into more detail about those if you want.