Download managers can in some cases be great to improve the speed and efficiency of your download. However, they work by establishing multiple connections to the server at once, so if you're downloading from a page that uses download-limits, your download manager will use up your limits in no time.
Even though you've only clicked a file once, your download manager might establish 5 unique connections, using up several of your attempts.
So, why are download limits even needed to begin with? Limits work as a layer of protection that prevents malicious attackers from flooding the servers. Having limits in place ensures that everyone can download safely, at a good speed.
If you've run out of download limits on one of your files, please make sure to disable any download manager you might be using before attempting to download again.