I'm finding this too -- buying one rat trap truck should earn me 2,322,000 XP but I'm always only getting 1 bonus level up box instead of 2.
I haven't worked out how many boxes I'm missing when buying more rat trap trucks, or the best number to buy to minimise the problem. It's safe to buy book burning mobiles 1 at a time, but of course that takes much longer!
Presumably this problem is affecting more players? Has anyone reported it to EA or found good workarounds/solutions?