You will find the crowbar in the chapter Unforseen Consequences, stuck in a sliding glass door.
Go ahead and yank it out of the door with the use key, then just bash the zombies' heads in and move on ahead.

The first appearance of a Vortigaunt will be behind a door (that will soon be destroyed), next to the dumpster guy.
Once you get close enough, you will hear them teleport in, then, they will destroy the door, and that's when you'll find your first subject.

Now for the last step in this guide.
All you have to do now is just walk up to the subject to get in range and to make sure they don't zap you with their beam things (as this is an unstoppable animation), and hold left click.
Don't worry about them punching you in the face, as long as they're taking damage, that animation won't play.

Now that the subject is dealt with, you are now free to celebrate.

Ah ♥♥♥♥, the military figured out you've murdered an innocent alient from Xen.
Don't worry, they're just as ♥♥♥♥♥♥ as the vortigaunts are.
Just hold left click on them and you're golden.