The Plant I work use's a three phase delta transformer to run there equipment I'm having trouble explaining why, on (A) phase the voltage is lower than (B) & (C) phases. Please help explain?

 

How much lower?

Actually, what are you measuring on each phase, and how are you measuring it?

Phase to phase, or phase to a neutral somewhere?

If your secondary winding is indeed a delta, you'll only be able to measure phase to phase. If it's a wye-wound, you'll have three phases and a neutral.

 

Because you are measuring A to the neutral which is center tapped.
For example in a 120/240 four wire Delta High leg.
A to Neutral is 120 but if you measure A to B, B to C or A to C you will get 240 in all.
You should buy Ugly's Electrical References booklet.