Ok, now I get it.

Missiles 101:

You have 4: Dumb fire, Heat Seeking, Image Recognition (IR), and Friend or Foe (FF)
Dumb-Fire: They go in straight line, do a lot of damage, but don't follow enemy ships.
Heat seeking: You must be enough time on the back of the enemy for it to lock on (the lock on the heat of the enemy's engines)
IR: You must have the enemy on screen enough time for the missile to recognize that enemy.
FF: You can fire this missile right away since it will lock on any enemy ship (it uses the communication frequency), however, if your comm system is damaged it might lock on you instead of the enemy (but I don't remember that ever happening to me).

So, the lock that appeared was when you had the Heat Seeking missile selected and it was when you were following an enemy.

You can change the missile type by pressing (M).

BTW, if you were flying the Scimitar, you should start shooting when the enemy is at 3000 kms, since the Mass Driver (the gray balls) only reach up to 2000 kms. Yeah very short range but they hit harder than lasers.

I do remember reading the manual thoroughly when I started playing but really don't remember learning much about missiles, so thanks about that. I might give it another shot but I think I honestly just suck at it, so I still welcome all the other recommendations.

I don't know about many past space sims, but there is a couple of games I am currently waiting for to be released.

https://robertsspaceindustries.com

I have never really been into the space sim genre, however I did play Star Wars Galaxies and it had a space sim element in the Jump To Lightspeed expansion which I enjoyed a great deal. So I started thinking about what kind of sim I would enjoy, and this one popped up. And the other one I am also interested in, purely because this is bigger than anything that has been brought out before is Infinity Universe.

http://www.infinity-universe.com/

Infinity Universe is still in development, however they are creating a game called Infinity: Battlescape which is using the same engine as the main game, but it is preceding the main game to garner interest in the hopes that it will pay its way for developing Infinity further. Hoping these release soon as I am very anxious to play them both just to see how they are done

Well, I will give you all the hints I remember (you must understand it's been over 10 years since I last played any Wing Commander, but I really liked it and I think I was average and I finished it many times so...):

1. Press (L) to lock on an enemy target and kill that enemy before attacking any other enemy (if you attack many enemies at the same time you might only damage their shield but not get through the armor so it is better to focus on one ship at a time until it is destroyed).
2. Avoid attacking the same ship as your wing-man (they usually tend to get between you and your enemy).
3. Avoid following the enemy when it is retreating (since his wing-mates will follow you).
4. The Scimitar is the slowest ship of all so you will need to use afterburner a lot (but be careful since you can run out of fuel.
5. I don't know what speed you use when attacking but when using the Scimitar and the Raptor you can increase the speed to the max (360 for the Scimitar and 400 to the Raptor).
6. When firing the Dumb fire missiles, do it when the enemy is coming head to head on you and when it is very close (less than 1500), it is easier to hit that way.

This is all I remember, so far, let me know if it helps or if you need more help.