Its just bad luck. You want to get money in when you have the best hand (usually not the case since unless you have a FH or better you are statistically behind all the combined draws) or can draw profitably to make the best hand. Maybe I should say you should get your money in when you have the best chance to scoop, like when you flop the nut low draw with the nut flush draw, or the nut low draw plus top set (even though you have a draw you are the favourite since you have the most pot equity). By the way I would not recommend 3 betting your AA hands unless you will make a similar play with a good unpaired hand or hand with a lower pair, because it gives too much away. In all forms of poker you have to have balance so that you're not too predictable. I personally will 3 bet my AA hands because I know I will also 3 bet AKQ2, A23K, A24J, A345, A234, A255 etc unless I think it would be unprofitable (you definately don't want to get the field to fold when you have a hand like A234ds!). The purpose for raising should mostly be to just build a bigger pot when you have a hand that has good drawing potential. When you have AA49, that doesn't really have good drawing potential, and against a field of four or more, thats a fairly junky hand.
The more players likely to call your raise, the more you should have a closely nit four card unit that will achieve its purpose best. A234, well you want to scoop with that so you're gonna need a low flop or the nut flush with hopefully no pair on the board.
Also if you find yourself continuing past the flop when you didn't flop that big after you raised pre, then you should try to plug this leak. When it comes 27Q and you have A3J9s, well you should probably reconsider your position, especially if there is a lot of action. Sure you got the nut low draw, but what else - its going to have to come running K, T, or T, 8, or 4, 5 if you want to scoop it, or maybe you hit running cards for trips and you're lucky enough to have made the best hand (I would say it mostly wouldn't be after a flop like Q72 since the lack of coordination combined with a lot of action means that you will very likely be against a full house on the river, since that is a good flop to fast play a set).
When you have a crazy person on your table, you should be pleased. They are playing AFC poker, and you do have an edge against them if you pick the right spots. But you have to be patient and perhaps overly tight in a tournament to overcome their aggression, especially if they play back at you playing back (I have played this type of player)! They are putting money in with hands that have bad drawing potential much more than you are, and that means that they will either get scooped or only get half the pot far more often if you are playing for the scoop.
It might be worthwhile to know that scooping a full pot is not twice as good as getting half, its four times as good. This is explained in the High Low Split section of Super System 1. This will encourage you to play to scoop more often.