On a certain song I am working on all most of the online videos and Tab I have seen play Dm Am Em but the CDLC version uses Dm Am and G is this just the charters querk (both Barr chords) or is it common practice for people to substitute 1 chord 

This more common than you would think. Published sheet music is sometimes wrong (eg Billy Joel). Tabs are often wrong and copied over and over. Self confessed YouTube experts are sometimes wrong. It can be confusing if you have strings\vocal\lead playing an E note over a G chord so it sounds like Em.

Trust your ear!

Listen to the bass player. If he's playing a G or D note, it's probably a G chord, but not always. Em/G is possible. If he's playing an E it's probably Em as you would likely recognize a G⁶.

Take note of where the bass, the chords and melody are moving ie before and after. There might be a progression/ scale run/ chromatic or something that makes one chord more logical than the other.

Look for a live performance on YouTube by the artist, you might be lucky enough to spot the chord being played.

I'm sure the charter made his/ her best effort to chart it right but they are only human.

Otherwise, trust your ear and go for it.

Dm Em and Am are all part of the key of C.  they are the 2 3 and 6 chords. 

G (5 chords of C) in place of Em can work musically. 

The guitar is a tough instrument to write for (unless the music is specifically written for the guitar)

this is because there a multiple ways to play each chord (inversions etc).

 

it could be the G is used as harmony to someone elses Em

an example of this is Shoot to thrill (ACDC).  the chorus is A G and D, but the bass plays A B and D (in parts).

Cliff is playing the 3rd of G and not G itself.