Flat roof shingle intersection

[mathew stouffer]

Tough to see in the photos, but is this installation correct. Looks like it could be trouble. House was two years old and no leakage was noted.

[Markus Keller]

Absolutely not. The easiest way to figure it is that it is always wrong 'when the water is running into, at, against the seam/joint INSTEAD of running over the seam.
I suspect the roof is leaking it just hasn't manifested itself yet at the interior. If it isn't leaking it will be soon. Those types of repairs/install work great while the caulk seam is intact. Once the caulk dis-bonds from either side, its all over. The shingles along the lower portion also look very saturated.
I would like to see a diffuser along that area to help disperse the water a bit over the lower roof. Instead of it just all running down into that nook.

[Nick Ostrowski]

The nice fat caulk seal is typically a sign of a bad install or leak as well. That was a poor idea on the part of whoever cooked it up.

[Bob Elliott]

Looks good for a plumbing job .
Never have I seen a valley like that.
My bet is they did a bad job on a closed valley and overlayed that DIY style to combat an issue with water in the attic.
Flashing goes under (not on top)

[mathew stouffer]

Bob, first time for me as well. :) Thanks guys.

Mat