I can't put a Block on an empty space

I try this on a map I've been playing since 1.4.7

I tried to put a block of Stone in an specific position, see the attached files

But the block just dissapeared when I put it. Also when I put a block over the fence below, all the missing blocks reappears in my inventory, sometimes.

1. Go to the location on the screenshot added
2. Try to put a Dirt or brick block on any of the four empty spaces on the floor
3. After trying to put several blocks, put a block above the fence below to recover the lost blocks