Learn Finnish: Se on nimenomaan tämä seikka, joka aiheuttaa ongelmia. - It is specifically this matter that causes problems.

This is a cleft sentence used to emphasize a specific part of the sentence. By extracting tämä seikka and wrapping it in Se on... joka... (It is... that...), the speaker puts strong focus on this matter as the culprit, contrasting it with anything else that might have caused the problems.

Could we use mikä instead of joka to mean "that" in this sentence?

No. You must use joka here because it refers back to a specific noun phrase (tämä seikka). You would use mikä if the relative pronoun referred to an entire preceding clause, a superlative, or a pronoun like kaikki.

How does the word nimenomaan work with this grammar structure?

Nimenomaan means "specifically," "expressly," or "exactly." While the Se on... joka... structure already highlights the noun, adding nimenomaan strongly reinforces that focus, insisting that it is this exact matter and absolutely nothing else.

Why is the object ongelmia in the partitive case?

Ongelmia is a plural partitive. The verb aiheuttaa (to cause) takes a partitive object here because the problems represent an indefinite, unbounded quantity. The matter is causing some problems, rather than a specific, closed set of problems.