I am not quiet sure if this is generated by KSP itself or by a mod, but I am getting a green rectangle on some spacecrafts:
Unfortunately, I cannot access those crafts from map view, meaning that I cannot switch to them, get information about their velocity or set them as a target. So I am trying to find the culprit to eliminate it. I created a test craft with the used mods and launched it, but unfortunately, I was not able to replicate the same issue.
I have version 1.1.2 and the following mods installed:
Contract Configurator
KSP AVC
Contract Pack: Clever Sat
Contract Pack: Field Research
Contract Pack: Historic Missions
Contract Pack: Kerbal Side Jobs
Contract Pack: Kerbin Space Station
Contract Pack: Tourism Plus
Kerbal Alarm Clock
MechJeb
Module Manager
SpaceY Expanded
SpaceY Heavy Lifters
Waypoint Manager
Orbital Science
Interstellar Fuel Switch
Procedural Fairings
ScanSat