I have noticed that if a mana bean (from ThaumCraft 4) of one type is inside a vacuum hopper and it sucks up a mana bean of another type, the second mana bean will convert its type and stack with the first mana bean. For example, if the first mana bean is associated with the Herba aspect, and the second is Lucrum, the lucrum bean will become Herba, leaving me with 2 Herba beans.

If I recall correctly, we had the same problem with luggage as well.

Yup, #267. Should be fixed in new builds. Please check with snapshot or wait for release and then update this issue.