Try using the Developers Toolkit to search the files on your server for the word "application". You'll find some legitimate uses such as "application_top.php", but the other results might point you to places to look.
https://www.zen-cart.com/tutorials/index.php?article=39

Or, maybe you're using a payment gateway where you've configured a Return URL in your gateway settings, and the "application/" folder is in part of that URL either by mistake or by default. It might be worth talking to tech support at your gateway for help with that side of things.

Hopefully that gives you some places you might look.