For something like this, if probably hit up YouTube and search metal roof + roof boot or pipe flashing
Two potential options.
Option 1. More caulk. It’s possible that the roofer did put caulk under the boot. Perhaps they only put calk on the perimeter. https://youtu.be/eidzG74VT5U
And that said, when I’ve had problems with flashing and my roof, the best thing to do is to get into the attic while someone pours water in specific areas. That’s the fastest way to know what specifically needs to be fixed.