ls command does not show app files in Applications or Utilities folders, but Finder shows the apps (macOS Catalina)

When I use the "ls -a" command in the /Applications or /Applications/Utilities folders, the only app that shows up is Safari.app in the /Applications folder. However, when I open the same directories in Finder, all of the apps are there and I can launch them and get info and everything. On a different machine this is not the case, and the ls command finds all of the apps. I have already tried re-partitioning the boot ssd, wiping all data on the drive, and performing a clean install of MacOS, however the problem persists. Even in the recovery mode the problem persists. I have verified with a different machine that four apps should appear in the Utilities folder while in recovery mode, however on this machine none do. At this point I have run out of ideas. If there is an even more factory reset I can do, I'm down to try it. The most confusing part is that the ls command fails to find the apps whereas terminal has no trouble. If you want any more specific information let me know and I will try to respond quickly. I apologize if this is the wrong place for this question, but I have never resorted to posting a question before, but this problem has me completely stuck. Thanks!