If your APs are just bridging clients from the wireless right onto your wired network, then you're going to see this from time to time. Clients will appear from different ports as they re-associate to other APs/cells in the ESSID.
I'm presuming you're talking about Cisco IOS here, based on the term "MACFLAP", which appears in their log messages when this happens.
For example: "%SW_MATM-4-MACFLAP_NOTIF: Host 0011.2233.4455 in vlan 123 is flapping between port Gi1/1 and port Gi1/2"
What this means is that the switch is having to "re-learn" an Ethernet MAC address out of a different port than what is cached in the hardware forwarding table. This takes a little CPU time for each event, and having it happen more than couple times in a row will cause that MACFLAP message to get logged as more and more CPU time is consumed.
However, this should not cause the entire table to be flushed or cleared. Just the entries for the flapping source MAC address should be getting affected.
Now, in your case, if this is an infrequent message and it's just wireless clients moving from place to place, I wouldn't worry about this too much.
To prevent this, some centralized wireless client termination would be needed. This way, frames would pop out onto the wired VLAN in a consistent place.
However, if this is happening frequently for many MAC addresses, it could be indicative of a Layer 2 loop which will definitely need some investigation. :p