As Mass said, Vinyl isn't intended to be watertight itself. Instead it sheds the majority of the water down its face, but a portion will make it through the joints (which aren't watertight or overalpping), so the real waterproofing (generally tar paper or Tyvek depending on age) is what sheds the remainder of the water behind the vinyl all the way to the bottom. That remaining water then will hit the bottom channel and collect/drain (the left side of your image) or simply drain if there is no channel present (the right side of your image).
The irregular water marks are just showing where that water is draining. No cause for concern. Number of reasons why it would come in certain spots and all just depends on gravity, the installation, wind, etc. A bottom channel helps keep the vinyl in place, but even with it you'd have the same water draining.
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