You probably have a shortcut that is shortening your route. Here's an example:
A = B = C
|| || ||
D = E = F
Say these are your planets. The longest possible route is A-D-E-F-C, five jumps. However, if you put trade ports on every planet, you will not get this route. You'll get something like A-B-C-F, which is one jump shorter.
Because there is a short-cut (A-B-C); because there is a faster way to get from A to C, you cannot have the longer trade route (A-D-E-F-C). If you demolish your trade ports on planet B, you will actually extend your trade port chain. If you have a sufficient number of trade ports, this can actually increase your income. Always build in a way to maximize your trade port chain. If you open a shortcut, you may actually reduce your income by building the new port.