A brief look at the literature shows that supersedure of queens has been a problem for many years. It was especially a topic of discussion in the late 1930s and early 1940s. I haven't had time to get into it too much but: 

VARIATION IN PRODUCTION. 

The 1935 shipment of packages was considered as an indicator of future possibilities for observing some of the specific causes of supersedure. While reports of 20 to 50 per cent supersedure of queens had been received in former years, and thus made supersedure an important problem throughout the province, no such situation developed in colonies produced by the experimental packages. The variation in production by colonies of the same strain as well as between the different strains was so outstanding that this characteristic received the most attention in the general absence of supersedure difficulties. Some of the colonies built up rapidly while others lagged behind throughout the season. 

SOME CAUSES OF SUPERSEDURE. 

An examination of queens exposed artificially to cold indicated that their physical condition may be so impaired as to cause reduced productivity, and even drone production. The effect of heat beyond a given tolerance may be likewise destructive. The injury or maiming of queens by the bees, due to excitement brought on by the colony being disturbed under unfavorable circumstances, is a very logical cause of supersedure or reduced productivity. Of 8 queens returned from the experimental yard for observation in 1937, 4 produced satisfactory colonies when introduced in the University apiary, 2 were injured physically sufficiently to have caused their replacement, and 2 showed no physical reasons why they were superseded in Canada and again when introduced into colonies at Davis. Sometimes the injures to a queen such as the loss of a foot segment or injury to the terminal segment of an antenna or an indentation of the abdomen affecting the ovaries are so slight as to escape average observation; and not all injured queens are superseded by the bees. Drone-laying queens from package bee colonies often had viable sperms in the spermatheca, indicating that they had been mated before being placed in the package, but had been injured by cold in a manner that would not permit the spermatheca to function properly in the release of the sperms. 

 Eckert, J. E. (1940). Studies of factors affecting package bees. Journal of Economic Entomology, 33(1), 77-81. 

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