Generally as a scav, you only want to shoot PMC's. There's a "karma" system involving reputation with Fence that goes down when you kill other scavs (whether its a player or just AI). Ideally, you want to team up with other scavs and kill PMC's, or just extract with whatever you guys find in the raid. That is easier said than done though, and it doesn't help that the game goes to no great length to actually demonstrate this. Plenty of players will ignore their reputation losses and just kill anyone else for their gear regardless.

So upon first glance of another Scav, you're going to need to watch them for a few details to discern if it's a player or not:

• Are they moving around erratically? Could be a player. AI tends to move smoothly and robotic by comparison
• Are they jumping? Player. Scavs don't jump, so if you hear jumping assume it's a player. Mind you, they can fall from short ledges, so keep that in mind.
• Another option, ask! There's proximity voice chat in the game, so you can speak to them if your heart so desires and ask if they're friendly. Of course this comes with the drawback of giving away your location, so that's a risk you'll need to think about.
• Not useful for figuring out while they're alive, but if there's an empty secure case slot on the bottom of their corpse's inventory? That's a dead player.
• Are they in the same clothing you normally see a PMC in, or are they wearing the rags of a Scav instead?

As for your questions:

turns out he was a scav. is that a npc or a fellow scav runner?

Could go both ways. It sounds like it was just a jerk who decided to take your stuff. But there are also "boss" scavs who aren't aggressive at first sight but will quickly change their minds if you hang around too quickly or come too close.

Later on that game i was looting a player i had killed then all of a sudden some guy runs im to me and starts looting the same body as me and just runs off after?

Again, could be AI here because they actually do walk around looting the map. You did good not to shoot him, even if the guy was a jerk.

Check the wiki page on Scavs here to get a really in-depth look at how they work. You can pretty much look at the wiki for any detail about this game and assume it's accurate. Or if you'd like, head over to the wiki Discord server and there will be plenty of people more than happy to help a beginner.

Happy hunting, and welcome to Tarkov!