Yes, “only” can be substituted in place of “just” in this case. I think they’re trying to say that it’s unusual/unexpected for the result to show that there’s only a lower motor neuron problem and not also an upper motor neuron problem with the sciatic nerve. It sounds like they want to wake this person up and see what the actual sensation is like. (Yes, I’m a medical geek.)

Does it imply that the knuckle not coming back is usually caused by more than one problem? I don't think so; I read it as saying that there is usually only one problem, in this situation...

Also (fyi) - "There ARE two problems..."

Also there's a problem with "which the sciatic nerve" - either it should be "'with' the sciatic nerve"... or, this sentence is incomplete.

"a knuckle that doesn't come back" might mean that it doesn't return to its normal position/ or it might be referring to some element of the 'test results' which came back regarding the knuckle....