Which word signals a problem?

actually

process

difficult

inexplicable

Well, that depends on a context, but i find that the last two have a potential to signal a problem, and the second last (difficult) more than the one after it:

1. He was overcome by inexplicable fear (there is a "problem" in the sentence, but can be attributed to other words).

His homework was difficult (this is a problem, so definitely a safe option)