The correct form would be John was troubled by something but I didn't know what it was. English usually forms sentences with a subject-verb-object structure, as in your first clause: John (subject) was troubled (verb) by something (object) The second clause is a little more complex: I (subject) didn't know (verb) what it (object) was. "what it was" here is an adjunct clause with "what" as a ...
In your context, the best relates to {something}, whereas best relates to a course of action. Plastic, wood, or metal container? What was the best choice for this purpose? Plastic, wood, or metal container? What was best to choose for this purpose? Either is acceptable, and the practical meaning is the same, but their referents, implicit not explicit, are different.
difference - "What was best" vs "what was the best"? - English Language ...
As a British English speaker, I find "What was that all about?" perfectly normal, after something said or done that I find inexplicable, either as a direct question to the sayer or doer, or, very often, as a rhetorical question to another bystander. In the latter case a possible response might be a shrug, or rolled eyes, or both.
idioms - "What was all that about" usage - English Language Learners ...
tense - What was your name vs. What is your name? - English Language ...
In my opinion, "How was the film?" would be probably met with a reply about the state of the actual place where you watched it, such as if there were any crying babies or there was a guy sneezing throughout the movie or if it was really smelly. "What was the film like?" would be asking the person about the ACTUAL film and not the surroundings. That is: were the scenes good, was it interesting ...