You get one link up/down message each a device thinks link state went down and another each time the device thinks link state came back up. This will generate a lot of messages very quickly, and are normal when cables are physically moved at switch or end devices.
I have had this error message caused by a number of different situations:
1. Autonegotiation issues. I set the switch ports to operate at a specific rate and it went away. Believe this was actually a NIC driver issue on the workstations. Recommend trying this on one or two "problem" ports and see if it solves the issue for those ports.
2. Electromagnetic Interference (EMI). Once, cabling went directly behind a microwave oven and another case was laid across a subwoofer. Errors only when devices were in use.
3. Cabling problems. Had a site trying to run Fast Ethernet on long runs over CAT 4 cabling. Works....very poorly.