Lead and metal both expand and contract with temperature which can put pressure on the surrounding wood and cause hairline split. Ebony and padauk are more vulnerable to these cracks than boxwood. Out of hundreds of chess sets that I have seen these cracks will eventually develop and are inevitable. Unweighted chess sets seem less vulnerable but if the wood has not been processed scientifically it will surely crack at some point.
Oh sigh, leaving aside scientific processing of wood, wood cracks. Repeated changes in humidity will crack it. Too much drying will crack it.
Lead IS metal on this planet. The thermal expansion coefficient of lead is a factor of about 0.000029 per degree Celcius so heating and cooling of the metal is not all that likely to impact the timber that its embedded in (imagine a 15 degree temperature change, on a 6mm lead plug, thats 6 * 0.000029 * 15 mm = 0.00261mm, technically what is referred to as not a whole lot). What is likely to have a larger effect is humidity changes in the timber (by about a factor of ten, ten percent humidity change in ebony, about 0.02mm per mm, you can get to tenths of a mm fairly quickly with that much movement, say 6mm thickness of wood * 0.02mm = 0.12mm, movement is along the growth rings, not along the grain so 6mm might be too small as a number). What makes the behaviour more interesting is that a plug inserted into the chess piece would slow the humidity changes and cause the edges to dry faster then the centre. The question is, do the cracks start in the centre (thermal expansion of metal) or at the edge (drying of the timber).
I'm not a fan of flaws either,but I realize that the vast majority of sets are not really very expensive compared to other hobbies( a couple hundred bucks on average,or less actually) so I'm basically rationalizing away any flaws.....but...Overall I'm quite picky and usually won't let a problem go without a good fight.