Dave,
        I'm not sure if these are the same mites which infest the pollen
balls and totally consume them in the tubes.  If highly numerous they
may be moving to the bees.  (?)
        Anyway, this type of problem has been reported in Japan.  It is
usually a problem in the Spring.  Unfortunately, the recommendation is
to wait until fall or winter and tear open the tubes and remove the
cocoons if there is any sign of mites.  Then soak cocoons in 5% bleach
for 5-10 minutes.
If the cocoon is intact, the solution should not penetrate and damage
the bee.  When dried, return the pupae to new tubes (nipple end out, of
course) and insert a small cotton wad in the end.  This will keep the
cocoons from falling out and is supposed to stimulate return to the tube
through glandular secretions released by the chewing out.
        If you are using reusable wood blocks, you can soak them too
before you reuse them.
        We have a terrible problem with Monodotomerus wasps, here. (NC)
        If you do it, let us know if it works.