So I constructed a B-chord using the intervals for a major, M3 and m3 in that order which gave me B-D#-F# from the CDEFGABC order I saw. Then I started to construct a B triad which gave me those three notes, i then extended it to a chord with a repeated F# and B, this is played on a guitar fret-board, the common a-shape barre chord shows 5 notes, is there a reason why when you play a B barre chord you cant extend your first finger to the 2nd note of the low E which is another F# which repeats another note in the order playing a 6th note?
There are some parts of your question that I don’t understand, such as the bit about “from the CDEFGABC order I saw.” However, if I’m understanding the gist, the simple answer is: no, there’s no reason you couldn’t add a low F# to the B major chord. For that matter, there’s no reason you couldn’t add E on the bottom of the standard A major chord position simply by hitting the bottom open string.
The reason this often isn’t done is that putting a note other than the root as the lowest pitch (especially the fifth of the chord as in your example) tends to muddy up the sound a bit, or even make it less stable sounding. In lead sheet terms, the chord you would be producing is no longer B, it’s B/F#. This is still a B major chord (well, in most musical styles and contexts; there’s some debate about other circumstances that are beyond the scope of this answer), but it’s a somewhat less bold or stable B major chord.
The difference is relatively subtle, and in many cases and genres of music it barely matters at all. In other styles (especially common-practice music such as that by Bach or Mozart), the difference is treated as very substantial. As always, if you’re just writing your own music, you should just use whatever sounds better to your ears. If you’re playing someone else’s music, and they haven’t requested a B/F# explicitly, it would probably be best not to add it and be faithful to the composer’s idea. If you’re playing in a band that includes a bass player, it matters less what choices you make along these lines, because ultimately it’s your bassist that determines the bottom note.
It's called an inversion. When the lowest note played is the 3rd(D#) then it's the 1st inversion and if its the 5th(F#) then it is called the 2nd inversion. There are many ways and fingering to play inversions on the guitar.