We need to cut these roofing penetrations so that they don’t leak and have problems. There probably five locations like this on the shingle portion of this roof that need repaired in this area to ensure the roof has no more problems.

Make repairs to the TPO wall here. 
To make these repairs we will need to remove this gutter, the gutter is not necessary it does not help with drainage, the main thing is that this wall could be leaking behind the gutter and this needs to be thoroughly examined to resolve this issue. The wall is TPO and it will need to be completely sealed to stop any roof leaks.