Both sentences are grammatically correct, but they have slightly different meanings due to the tense. * A. "I thought something bad had happened to you" (Past Perfect) indicates that at the time you thought this, the bad thing was already completed in the past. This tense emphasizes that the event (the bad thing) happened before your thinking. * B. "I thought something bad happened to you" (Past Simple) is more straightforward and can be used when you don't emphasize the timing of the bad event as much. It suggests that the bad thing and your thought about it might have occurred around the same time. In general, the Past Perfect in Sentence A is more formal and specific when you're clearly talking about something that happened before another past action (your thinking).

B. sounds more informal and slightly more colloquial. B. is more typical in everyday speech or discourse or casual conversation.

A is best for formal. B is best for informal.

Those are two perfect sentences. Neither is better than the other. Which to use depends on context. Sentences are NEVER spoken without context. There is almost always talk that comes before and talk that comes after. There is almost always a place, time, and mood. The people have some sort of relationship to one another. Words are never spoken in a vacuum.

It's interesting people are saying B is more colloquial and A is more formal - I would say B is ungrammatical (or at least "semantically anomalous") because it implies the bad thing is happening at the same time as the thinking. A is the one to go for. I'm not aware of people using B at all in conversation, although in this particular case the difference in sound would obviously be very small.