We use past perfect when we want to talk about something that happened before some other event in the past, and the order of events is not otherwise clearly indicated- for example by conjunctions like before, then, next and later.
I finished the wine when he arrived. -simple past
This means that he arrived and I quickly finished the last of the wine. The two events (him arriving and me finishing the wine) happened at roughly the same time- both in the past.
I had finished the wine when he arrived. - past perfect
This means that I had already finished the wine before he arrived. His arrival is in the past, and my finishing the wine is even further in the past.
Mr. XYZ came to my desk and he had some issues with you.
In your sentence, there is no other event that "Mr XYZ came" can be before, so simple past is the correct tense, and you cannot use past perfect.
before "some issues": both are grammatically correct and meaningful, but have different meanings.
had is simple past, and indicates that Mr XYZ had some issues at the time you spoke to him: it doesn't indicate whether he still has those issues. Maybe you managed to calm him down, maybe not: the use of had doesn't tell you.
has is simple present, and indicates that Mr XYZ still has issues, and presumably must have also had these issues at the time you spoke to him.