The title might sound a little silly, but I have this confusion: When someone says, "Join document A with document B", does it mean document A should be first or document B should be first?
The answer lies in the function word "with", not the word "join".
Join A with B
Would normally be interpreted as meaning to produce "AB".
However we can flip this interpretation by changing "with" to "onto":
Join A onto B
Would normally be interpreted as meaning to produce "BA".
When in doubt, you can use the words "prepend" and "append" to be explicit:
Prepend A to B
Means produce "AB".
Append A to B
Means produce "BA".
It's ambiguous enough that whoever made the request shouldn't have a problem if you ask for clarification.
As with just about everything in English, it depends a lot on the context. For instance, the fact that you have listed documents whose names have a natural order (A then B), you would expect that the person wants the first document in the list order to be first. Moreso, if (s)he want them to be joined out of order (i.e., B then A), this should have been explicitly identified in the request.
If the documents being joined have no order, e.g., join the mango document with the apple document, then you shouldn't go wrong if you join them in the order mentioned—i.e., the mango document first then the apple document.
A different context would be where the two documents contain 'mergeable' information (e.g., lists, database records, etc). In this situation, the join request would result in a document that has items from document B interspersed with items from document A in list order, or record order.
A (slightly) less ambiguous version of the request would be to join document A to document B. In this case, I would expect the first named document to be added to the end of the other document. Again, if the documents were named 'A' and 'B' (or 1 and 2, or anything that inferred order), I would still double-check that the person didn't really want 'A' before 'B'.