Contraction: "it've"

Solution 1:

It took me a while to wrap my head around this, and eventually I realized that that's because "Could it have come from the cave?" sounds clunky to me anyway, so initially "it've" did as well. Either "Could it be from ..." or "Could it have emerged from ..." sound more natural to me.

To get back to your original question, does "Could it have emerged from ..." be contracted to "Could it've emerged from ..."? Even though it looks strange written down, it sounds perfectly good to me and the writing is unambiguous, as there's no other words "it've" could expand to here. So I'll say that it's an unusual but perfectly comprehensible construction.

Solution 2:

As a copywriter, my rule of thumb is, 'Does it sound natural?' i.e. the rule of euphony.

'It've' sounds clunky to me, as does 'it'd' (it would). So I wouldn't use it.

Solution 3:

It sounds fine to me. In your example "Could it've come from the cave?", the subject of "could" is "it", and so if there were subject-verb number in the example it would have to be between "could" and "it". But "could" does not have a distinct singular-agreeing form. "(ha)ve" in its position after the modal "could" cannot agree with the subject of the sentence.

(I didn't understand any of the comments -- maybe I'm missing something.)