Several of these explanations have been mentioned here - with the most common in my experience being individual keywords to which the advertiser has given a Max CPC setting higher than the default for the ad group. This individual setting always trumps the default setting.
IMO, it's best to address this concern directly to the AdWords support team, as they can look at the account and get to the bottom of things - whereas here, well, we're just guessing. ;)
AWA
Once I found out that the reason for this anomaly was that I had individual keyword level bids which were much higher than the adgroup bid (which was my mistake)
The other time this happened was for a placement targeting campaign. The max cpc bid for a particular site in that campaign was set as 15 and the average cpc I got was 19. This was definitely not my mistake. Also the campaign was in cpc bidding strategy. So, the issue of getting clicks at higher cpc earlier would not be the case here.
And the other thing which happened is that after I paused the adgroups in question while I tried to figure out what was going on, they continued running and generating clicks.