1. Excess headspace can cause flattened or cratered primers with ammo that's nominally within normal pressure limits.
2. There's a chance here that we have a case of the difference between 5.56 and .223. 5.56 chambers and leade are a hair looser; .223 is tighter. The permissible max pressure for 5.56 is also higher than that for commercial .223. Most ARs, unless otherwise specified, are made with 5.56 chambers. If you were loading before for a 5.56 chamber, then that's why the primers didn't show up then. Also possible that the WWB was loaded to 5.56 specs instead of .223.
And then sometimes, stuff just happens. Couple months ago I shot a box of TZZ Israeli milspec .45ACP in a S&W M25-2 without using the snowflake clips. The primers were flattened much more than you usually see in .45ACP. They were flattened more than the same ammo fired in several 1911s. Some vagary of the ammo/headspace combination on that particular gun, I suppose.