If something bad happens to you it is not because God wants you to suffer but because God has given evil dominion over this place in order to facilitate free will and choice.
God wants to be reconciled with every person but also wants that reconciliation to be chosen and not coerced.
The suffering of innocents is just an extension of this idea.
The Book of Job in the Bible for example posits that God is almighty but not at all fair. He basically causes Job to suffer on a whim. Not out of some kind of theological necessity, but simply as a cruel experiment. There is no paradox here, because there is no claim that God is always just and benevolent.
This isn't technically true. What God does is choose to not prevent Satan from testing Job. I'm not making a judgement about whether this would be considered cruel or not, I just want the facts stated clearly.
And, Job himself said, "Though He slay me, yet will I trust in him" (Job 13:15).