before the battle sometimes the automatic script or a clan member accepts everybody who has applied by then, but then in the rolecall more high level people or simply people they know from previous battles come around and might get preference, had it happen to me a few times as well. A few months ago I could get on most battles I applied for, now I get disaccepted during rolecall quite often, so I ended up not applying at all.
Basically: dont take your place for granted until you get accepted during the rolecall.