Where exactly? No, should not be any. Both batteries are pretty new and not much used. Maybe what you see is glue remains from the cover tape? Or that dark area left of the orange cable is in shadow. I had light coming from "all over" when I took the photo, from the circular lamp near by from my magnification lamp. It throws shadows here and there when taking macro photos.

I think that system is not good though. The blue cable should be get somehow other side of the circuit board. It is little too risky now if something nasty happens, like one drops the phone to water or smashes to the rocky ground or something and the 2nd battery will cause the 1st battery to short cut.

Edit:
status update:
The system has been running now 19 hours and the charge level is 49% says BatteryGraph. I had SleepAnalyser recording 8 hours and have used the device quite much today, couple of reboots. The capacity wise the hack seems to work and comparing the decrease-angles of BatteryGraph history, this now seem to give 2x effective usage time.

In the pic below, one can see little better how the original BL-5J battery looks from the top. There is no really other places to put that blue (-) cable. The red (+) cable has a good place on back of the connector, or even anywhere of the outer shell.

I wonder if somehow the blue (-) cable could be attached to the middle pin but same time able to insert the battery inside N900 battery hole and have it working. Maybe with thinner cable it can be done, but the cable has to tolerate that 1A.
Maybe replacing the edge "cap" (the black one in the pic) with something totally else, or modifying it to have a hole on top of the middle pin.