When we played on my server, light blinked, computer reloaded, after that when I reloaded server I seen this holes, chunks is there, but looks like it not, server won't let pass through it. When you touch invisible block it pushes you back. In survival it makes damage when touching it. Whatever I tried, holes still there, F3+A, server reload, nothing helped. In creative if you jump in hole from sky you will fall slowly.
This problem occured after server doesn't properly stopped. I seen something like this in earlier versions, but after reload it fixes itself, this can't be deleted by any official method.
P.S. Sorry for bad english. =3