Ran into a annoying problem, have been having this problem multiple times of past, and never remember what the fix is. So now its on the blog for next time that i need it. Use the shell option in the freenas installer, the disks that i wanted to install onto was ada0 and ada1.
1. sysctl kern.geom.debugflags=0x10
2. dd if=/dev/zero of=/dev/ada0 bs=512 count=1 && dd if=/dev/zero of=/dev/ada1 bs=512 count=1
This will wipe out the sectors that keeps the partition schema and afterwards you can install FreeNAS without problems.