Is it a hatch? I have had a few leaks that were caused by the sealant that connects the roof panel to the rear wings going bad over time and causing a leak. These cracks are hairline and usually appear around the boot or hatch area or occasionally on the roof under the beauty trim.
I would suggest looking at all the points where sealant is used to connect body panels on the upper bodywork very carefully, lift the trim and check along there for signs of the paint having cracked. If you do find a crack, carefully clean it.
I had good success using Captain Tolleys creeping crack cure backed up by some polyurethane sealant carefully wiped into the joint.
You may need to check under the roof trim inside to see where the trail starts, summer time and a hose is a good time to check with some baby powder dusted to show any water trails.