Learn Russian: Мы говорили о том, что у компании есть проблемы. - We talked about the fact that the company has problems.

In Russian, prepositions like о (about) cannot attach directly to the conjunction что (that). Instead, you need a pointer pronoun то to take the preposition. Because говорить о (to talk about) requires the prepositional case, то changes to том. You can think of о том, что as literally meaning 'about that, that...' or 'about the fact that...'.

Does the comma always go before что in this structure?

Yes. In Russian grammar, a subordinate clause (a dependent part of the sentence) starting with что is always separated by a comma. When using pointer words like о том, the comma always goes right after the pointer word and before что.

Why is the company in the genitive case (у компании)?

This is a refresher on the standard Russian way to express possession ('to have'). Instead of a verb like 'to have', Russian uses у + [owner in Genitive] + есть + [owned object in Nominative]. So 'the company has problems' translates to 'at the company there are problems'. The genitive of the feminine noun компания is компании.

Why use the imperfective verb говорили here instead of the perfective сказали?

Говорили focuses on the ongoing process or the duration of the conversation ('we were talking' or 'we discussed'). If you used the perfective сказали, it would mean a single, completed action, translating closer to 'we said that the company has problems'.