not seeing all traffic on SPAN port on Cisco switch

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Copying packets to a span port is one of the low priority tasks in the switch. If there's a lot of traffic packets will be dropped on the span port, not on the switch ports.

If there's a lot of traffic on the monitored interfaces this may also overload the span port, resulting in packet drops. For instance monitoring both ingress and egress traffic on the switch fabric doubles the amount of traffic on the span port. So if possible, look into the performance data of the switch to see what happens on the span port.