They could have meant to say "What's the matter." As in "What is the matter." but with a 'what + is' contraction. It could have been a typo if you read it online. What the matter is neither natural sounding, nor grammatically correct.

It is funny...The first idea to come is obviously that they were somehow influenced by WTF-like constructions. But unlike native speakers, I can't predict or exclude the possibility of the two constructions interacting/mixing in their minds:(