I'm judging by fuzzy photographs, but the flashing seems to have been done incorrectly. When done right, shingles and step flashing alternate such that any water running under one is still on top of the other. Here we see very large metal flashing laid completely over the shingles, so that any water running or blown under the metal encounters no further drain plane beyond the edge of the shingles.
Here's a diagram of where I'd have expected the shingles to overlay the metal (and lay under the flashing above):

Here's a good example of proper flashing:

There's also a diagram of the step flashing on that article.
I can't be sure this is the problem, and I'd hate to accuse your tradesperson of negligence, but that's where I'd start. Read and understand that article, then compare your situation.