I just got my 1911 SA used and it came with two mags.
How can I tell if they are factory or aftermarket?
On the follower there is a little "pebble" sticking up. This makes loading the first round little hard because I have to get case over the pebble.  What is that for and can it be removed with no problems? Do all magazines have it?

dimple and keep it.

You need the dimple.  It's there to hand on to the last round.  It works.  

Springfield mags will probably be marked with 45ACP on the side near the bottom.  The base plate will have two threaded holes for a pad.

Springfield mags are Check-Mate 7 round wadcutter mags.  

A Wolf 11lb spring is great in those mags.  Those mags (with an 11lb spring) are actually what I consider to be the most reliable 1911 mag on the market, bar none.

Just don't get too aggressive with slide lock reloads, the base plate bends pretty easily.

And don't touch anything associated with your 1911 with a Dremel, file, sandpaper, or hammer.

The dimple is there for a reason, it's to assist keeping the last round in the mag under control during feeding (when mag spring compression is at it's weakest)

I am doubting it is a S.a. mag.

I was thinking the dent might have been a defect.

Where can I get replacement parts for the 1911 mags?

Any harm in leaving them fully loaded all the time?

What is a wad Cutter magazine?

I just looked at my two magazines that came with the pistol it does have 45 acp close to the bottom and on the floor plate there are two holes. So I am guessing they may be original.  I just got two more mags in and they do not have the demple on the follower.  But when I load them they are tight. On the bottom of them is stamped colt 45 auto. They are blue. Wondering if they could be mil surplus

Not mil surplus.  There are basically no mil surplus 1911 mags readily available anywhere.  If they don't have the Colt horse on 'em and a C or M stamped in the corner of the base plate then they're knock-off junkers.

If you want Springfield mags, go to topgunsupply.com and order Check-Mate 7 round wadcutter mags with welded base plate, blued steel.  The Wolff 11lb springs come from gunsprings.com

"Wadcutter mags" refer to the feed lips.

There are a few different kinds. "GI" profile also known as "ball mags", "wadcutter" type feed lips, and "hybrid".

GI feed lips release the cartridge earliest. Wadcutter feed lips release the round later on. This came about in the 60s, and 70s in response to semi-wadcutter loads, and rounds with a shorter overall length.

Hybrid mags release the round somewhere in between. I like wadcutter mags. They work well for me.

Samuse is right.

DO NOT REMOVE THE DIMPLE.

FYI I did just get an e mail from the cmp they have usgi surplus mags new in wrapper for $8 each limit ten. If you don't mind a seven round mag they might be a good choice for a cheap but effective magazine

http://forum.m1911.org/showthread.php?11580-Magazine-Function-The-Dimple
This should explain the "Dimple"

Sproingfield ships decent mags with their guns. They used to offer a discount on extra mags with the purchase of a gun, don't know if they still do, but you can buy them from the company web site online.

For new mags I like Wilson Combat, but at the same time my factory Kimber mag hasn't given me a single issue.

And as others said don't remove the dimple as its there to control last round feeding.

Best place to buy parts for the mags?

gunsprings.com for springs.  

If you need anything else, throw the mag away and get new ones from topgunsupply.com.

I'd recommend buying yourself a few Wilson or Tripp magazines.

I've been shooting custom 1911s for 20+ years and won't use anything else.

They are the cheapest way to increase reliability in any 1911

Tripps maybe.  Wilsons no, not even close.

These will help:

1911 controlled feed principles
1911 magazines, part 1
1911 magazines part 2

I'd say there are a lot of skilled and experienced individuals that use Wilson's mags.

They don't overcome every issue but if your gunsmith can't get your gun to run on Wilson mags I'd question downgrading to a lesser product.

I set up a 1911 for absolute reliability and they will run on Wilson mags, they'll run on any mag that works.

Wilson mags just don't work for very long.  I used 'em for a couple of years.  I would wear out a set of springs in 8 47s in six months, the mags would all have spread lips at the end of the year.  Granted, that was 10-12K in that year, but the mags were done in a year.

I have trouble-shot many 1911s with 'extractor issues' and 'FTRB' malfunctions that were directly tied to 47Ds, and lately ETMs with weak springs.  The feedlips are too short, the springs are too weak, the followers are too smooth.  They just don't hold up.  Most 1911s are Kimbers, Springfields, and Colts.  Most of them will not run reliably with 47Ds and factory FMJ.  They may seem to, but they're inertia feeding and the extractor will break or lose tension before long.

I had a guy call me Saturday about a broken EGW HD extractor that Alchemy installed.  Had a measly 15K on it.  Mags?  ETMs.

I'll agree with samuse on this the springs on Wilson 47d mags are shit. Replace them with Wolff extra power springs.