The size of the port check was missing from the calculation. It should be only present if the potential port size is >0 - to allow for 0 port that can build.
First time I noticed this phenomenon was when I was testing the RHS mod. The mod had added a Naval HQ in Chungking assisting in riverine operations. I somehow overlooked the existence of this HQ. The result of this HQ addition was that several inland bases in Chungking's vicinity had 1-3 Naval Support present. The bases were empty of troops. I was thinking the mode was somehow broken. Then I played stock, noticed the Dambulla anomaly and finally connected the dots.
So yes, it is a display thing, but I kindly beg you to make WITP:AE perfect for the newbies out there.