How to fix leak from flat roof under lead flashing
Your guess may be correct. From what I can see from the photo the valley flashing doesn't appear to extend all the way down the pitched roof (although that may be from the angle it was taken).
What it also can be from is the chimney above the flashing. Flashing chimneys is extremely detailed work and must be done properly.
Extend the valley flashing if necessary. Check for loose shingles and nails. Remove any obstructions impeding rain flow from the flashing and gutters. Look at chimney flashing; i should be embedded in the bricks mortar joints.