I get this every time I log in
Which is an application that I downloaded a while back. But I can't locate it in my applications folder and I also cant see it in this:
How should I go about preventing this?
Check the Activity Monitor first to see if the App is running.
( Applications > Utilities > Activity Monitor.app )
If you can/can not find it there, it may be a launchd-process that has some special name.
Open Finder and hit CMD+SHIFT+G. Check these Folders:
Delete the file you are looking for (App-Name / Company)
but be careful - do not delete any random file.
Restart your Mac. If it still popp up, it is hidden somewhere else. I don't know what you installed, maybe it needed admin priviliges and is therefore located in the System/Library/LaunchDaemons folder.
Other Folders that may contain your app/script.
/Library/StartupItems /System/Library/LaunchDaemons /System/Library/LaunchAgents
You could also check the logs via the Console Application.