These are two different word forms. "чем" and "чём" are declensions of the same word "что". They are pronounced differently: чем [chyem] (instrumental), чём [chyom] (prepositional). Russians often write the letter "e" instead of "ё" and this makes learners confused.
Your example should be written "В чём проблема?" ( "В чём" is pronounced [f chyOm] )
Here's the declension of что:
case singular
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nominative что́
genitive чего́
dative чему́
accusative что́
instrumental че́м
prepositional о/в чём
There is also conjunction "чем", which is normally translated as "than".