Hello there, you can link me to any other forum related to this subject or call me noob or anything or hate, however as i'm new to learning guitar and this site I have a small issue :P

Recently I started to practise on the Fender Squier (Apple Red model) 6 String Electric guitar.

As I currently cannot tune by ear, I have the Fender FT-004 Tuner (Detects tune via vibration).

However, this morning as I was tuning my guitar to standard, my guitar doesn't sound like its in tune. I set the tuning scale to average C (Chromatic). When I play the low E string, its in tune, however when I'm fretting a few up, the tuning doesnt sound right, the tuning pin indicates its un tuned and playing chords sound terrible.

Is there an issue to fix this or is it just me?

You need to check the intonation. Google it, there are many tutorials available online.