It looks like a newer roof with and older boot with tar as sealant…a maintenance issue, at this point, or replace it. The flashing apron is usually visible, too.
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Modern flashing is meant to last the life of a “single” roof and therefore must be replaced when roof’s coverings are replaced. Rusted galv steel will develop holes. Premature leakage is in order.
You first!.
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most likely it has 2 layers of shingles. the second layer (top Layer) was not installed under the flashing correctly, as that would have taken more time to install it correctly.
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Improper flashing noted. Have a competent roofing contractor Replace with a proper one
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Too easy…
Straight to the point for a competent contractor once he looks at it