HTC One M9 :: App Is Duplicating Files On SD Card

I have something going on with an unknown app where the downloads folder has hundreds of duplicated files. My downloaded files folder is up to 3447 and, I'm only guessing here, but I think it only had somewhere around 500 before this? I'm not sure which app is doing this. This is occurring in two places and both are on the SD card. The first is the downloaded photos and the second is the downloaded files. It may be that the two are one and the same just that the photos folder only shows the downloaded photos from the downloaded files folder.

Also, there are photos that I have never seen before, a woman in a blue dress, a truck on fire, and others that I do not recognize. Additionally, I have noticed that other folders on the SD card are being accessed and changed as well because the dates of files inside those folders do not make any sense such as a photo that I took two weeks ago appeared yesterday as being taken yesterday. The date of that photo was dated for yesterday...

I have deleted apps, disabled apps, and stopped email from checking for new email (changed it to manual only). I thought it might be a setting in my email as a lot of the files are downloaded files from my email, but it continued after that. I'm not sure what to check next.

Is there an app that tell what apps are accessing what folders? Or is there a way for me to figure out which app is causing this? I hate to even say this, but I remember when I switched from the iPhone 3G to Android. I thought my Android blew the iPhone away until I figured out that Android does not allow me to limit the access to certain things on my phone. If I want an app, I either allow it to access whatever it wants to access or I don't download the app.