I've seen something similar myself, if you have two symbols with the
same refdes AND the same pin numbers, you get TWO nets for the common
pins, not a combined net.  Here's a schematic with such a case:

http://www.delorie.com/electronics/m16c-26-adapter/

I have one "connector" symbol for the MCU, *and* one "logic" symbol
for the few connections I want.


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