What's happening here is your players are treating your "disadvantage" system in the same way that they treat all the other pieces of character creation: they're trying to build a good character.
Let's take stat point allocation as an example. Suppose someone is playing a fighter, and they choose to have their strength score be high, and their wisdom score be lower. We could say: "That's so lame! You're min-maxing your stats to make a better character! You should be playing something more realistic, like a fighter whose best stat is intelligence!"
Now suppose our fighter character is allocating their skill points, and they choose to put a lot of skill points in "melee combat". We could say: "That's so lame! You're min-maxing your skills to make a better character! You should be playing something more realistic, like a fighter whose skills are in food preparation and eighteenth century literature!"
And now our fighter character is choosing disadvantages, and they choose "afraid of spiders" and "can't tolerate spicy food". We could say: "That's so lame! You're min-maxing your disadvantages to make a better character! You should have taken 'prone to epileptic fits in the middle of combat' and 'pacifist'!"
In other words, the problem you're having is that [your players believe that] your game rewards more competent characters with greater success. This is not unusual: nearly all role-playing games do it. If you really want to fix this problem for good, you need to make it clear to your players that their characters' competence doesn't matter. One option would be to switch to a game like Fiasco where it's expected that everyone's character will die horribly by the end. At the minimum, you'll probably need to stop having combat in your game, because combat will usually reward the characters with the best combat stats.
If you're not ready to completely eliminate the "more competent characters succeed more" thing, a good hack is to use a simpler character creation system. You could use something like Dungeon World, where the aren't as many character creation choices, so there aren't as many decisions to min-max.
But, to formally answer your question: if you don't like people min-maxing their disadvantages, the best solution is to not use a system that has disadvantages. You can switch to a game system that doesn't have a "disadvantages" feature, or you can stick with your current game and simply house-rule it that part of it away. (If you house-rule it away, you might need to award your characters some bonus experience, to make up for what they lose by not taking disadvantages.)