Why do you feel the need to be forgiven for your incomprehension? God Himself (or Herself, or Whatever) said that you can't understand Him (Job again).
Or, if you're talking about asking for forgiveness for thinking about these things while you're supposed to be praying, if you're not going to be thinking about these things when you're praying, what should you think about when you're praying?
Just use that painful frustration of incomprehension and channel it into your prayer. Prayer is talking to God, after all, and you can say whatever you want. "I don't understand You, and I hate what you're making happen in the world!" is fine. Any strong emotion, be it positive or negative, makes prayer better.