Improperly Installed Flashings
Caulking is often used in conjunction with step flashing around chimneys. Caulk has a relatively short lifespan, so it will need to be inspected frequently.
The flashing around your pipes, usually lasts around 15 years if installed correctly. You should periodically check your roofing flashing, and look for other materials that seem out of place or improperly installed to prevent roof leaks and other roofing problems.
To repair this issue, your roofer will reinstall the flashing or other roofing materials using industry-standard best practices.