If I'm understanding you properly, the problem is that there are repeated pairs of values in your matrix? E.g., [4, 8] appears twice, in columns 25 and 26.
There are only 30 possible permutations of pairs drawn from your 6 numbers, assuming that order matters (so [8, 4] is different from [4, 8]). I like using the arrangements package for combinatoric tasks (there are several other options: see this great review at Stack Overflow):
library(arrangements)
# Create the sample population
sample_popu <- c(8, 3, 1, 11, 4, 7)
# Find all the permutations of selecting 2 items
# from `sample_popu`. replace = FALSE by default
# (see ?arrangements::permutations)
permutations(sample_popu, k = 2, layout = "column")
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> [1,] 8 8 8 8 8 3 3 3 3 3 1 1 1
#> [2,] 3 1 11 4 7 8 1 11 4 7 8 3 11
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
#> [1,] 1 1 11 11 11 11 11 4 4 4 4
#> [2,] 4 7 8 3 1 4 7 8 3 1 11
#> [,25] [,26] [,27] [,28] [,29] [,30]
#> [1,] 4 7 7 7 7 7
#> [2,] 7 8 3 1 11 4
Created on 2018-09-24 by the reprex package (v0.2.1)
These are obviously not in a random order — arrangements::permutations() puts the results in lexicographic order by default. I don't know if that matters to you?