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.

The trade route will seek only the longest direct route.  Or: It chooses the longest "shortest-path" between worlds.  Therefore, if the route makes a loop, it will decrease in length!   So avoid putting ports at key planets, forcing the trade route to take the long way around.  Carefull planning can increase your trade income potential considerably.

Experiment by scuttleing key planets' trade if you think it is shorter than it should be and reobserve the displayed trade line as you hover over the income icon.  (PS see my karma for some good old discussions of trade).

Edit: Oh, it looks like Darvin beat me to it, and he explains the same thing well.