I have seen this same thing when I go after just a small class (15-18 players). One thing I have noticed is that if you check the Top Classes Report the last week of recruiting most schools have 17-20 players, but when you check again on signing day most schools have 25.
After I noticed this I purchased the time saver that shows how all schools are spending there recruiting time. This was very telling. You have some guys who gain interest with there top school, but the school is not spending any time recruiting them. These players are actually easy to find in the game by viewing there top schools. If the player has green interest but no scholarship offer he is probably one of these guys.
Basically the kid really loves that school and is hell bent on going there but the school either has better targets on there board or do not need his position in that years recruiting class. This might seem like a bad thing but actually when you find one of these guys you have a decent chance of stealing them away if you recruit them hard enough because they will be on the market until they get that scholarship offer. If the school just has better targets and they miss out on signing those players there is a chance that when they go out and add new players to there list they will find this guy and offer him a scholarship.
After looking at how the extra signing works, it appears to go by prestige. The higher prestige schools will get first run on these "walk-on's" and the game goes down the list filling assigning these left over players to schools.
Thinking about this from a balance stand point I actually like how this is implemented. Personally I like the powers staying good and new programs slowly emerging. This allows if to happen, but at the same time allows the user a large recruiting pool because there are players out there who will not be just snatched up by the big schools right from the get go.