When I started my Octoprint this morning there were a lot of files that had been uploaded, I'm thinking maybe it's the new updates. What am I suppose to do, anything or nothing?
I guess you are talking about the printable files? Updating OctoPrint doesn't upload files there in any way.
If there are files the that you (or anyone else with legitimate access to your instance) didn't put there through uploading them via the web interface, the watched folder or some automatic upload from a slicer or such, I'd assume that someone got access illegitimately. In which case it's time for a) finding out how/from where (secure those logs!), b) tightening down security (port forwards? Disable them, set up a VPN or at the very least http authentication) and c) redoing your install since it might be compromised in other less obvious ways, making sure to update to the current stable version in the process.
I figured it out and what it is is that I had put my SD card in the slot to test something and forgot to take it out and it is showing me all the files that were on the SD card. Sorry about that.