what sealant did you use?
The pic where you peeled it back with the finger is typical of poor cleaning before sealing. You'll have to pull it up and clean properly and then reseal. Does the vent stack actually have any sealant touching it? The whole idea is to seal the gap between it and the roof, it doesnt look like that happened.
If you did the work, you have a lot to learn about sealing before it rots the wood in the roof or causes the sidewalls to delaminate. If you paid someone to do that I wouldnt be going there ever again and I would be finding someone to redo it before the rains start.
