This might be an issue not even related to Reposilite but I don't really know what else may cause this, but:

I uploaded an artifact with the version 1.0.0. I later decided to reupload pretty much the same artifact but with small changes and I decided to leave the version the same (1.0.0). Currently no matter what I do the previous version is being downloaded. While I can easily download the correct artifact from the VPS, trying to download the artifact using the frontend will result in the wrong one being downloaded (even though the frontend shows the correct file size etc.).

Is there something in Reposilite that may be causing this?

For now I tried completely removing the artifact and uploading it one more time. I also tried rebooting Reposilite with hopes that cache will be cleared (if cache was indeed the issue).