I see they cut some and wove some in the thrd or 4th pic. [:-party] I wouldn't feel much confidence in any of that addition roof. I will bet they fudged on the underlay as well. Who knows how many nails per shingle and where they placed them. To repair, they need to bend the old shingles up to nail below, as David described it, mucho trouble that might still lead to leaks. I would tell them what the roofer will tell them, tear it off, sorry about that. They can cut the large side, but it won't get renailed all that well. A roofer wants to guarantee his work, tough call there.