The use of the subjunctive in your sentence is normal because the main clause of the sentence is a question.

As a rule expliquer que is always followed by the subjunctive if the main clause is an interrogative or negative clause.

Comment expliquer qu’il fasse si chaud ?

That being said, I would not be surprised to hear some people say:

Comment expliquer qu’il fait si chaud ?

but it wouldn’t sound natural to my ears, probably colloquial.

When the main clause is affirmative, both, indicative and subjunctive are possible. The subjunctive is probably more frequent, especially if the explanation is shown as someone else’s thought:

C’est la façon dont mon professeur explique que le français soit si compliqué.

Having the indicative in the sentence would probably show a greater degree of certainty.

C’est la façon dont mon professeur explique que le français est si compliqué.

This is adapted from p. 376 of the Dictionnaire des pièges et difficultés de la langue française