In reality, all those would be worse than a bee sting. And you can't contest that.
But, since we're talking about an animated movie, where reality isn't very important, maybe the "terrible bee sting" does have some merit inside the LBT universe. So, let's take a closer look.
Since none of the injuries (including the bee-stings) left any long-term marks on the characters in LBT (with the possible exception of Petrie), the only way we can judge the severity of a injury, in-universe style, is the amount of acute (sudden) pain it would cause. So, during an injury we have to see the character's reaction.
And since we didn't see Spike's and Ducky's reaction during the bee sting, and having already established that we cannot rely on reality regarding injuries in LBT either, we cannot know how painful it was. Or can we?
What was the most severe reaction of all? Ducky falling unconscious after hitting the hard surface of water in LBT 4 (water seems very hard when you jump from a high point, and it is painful). She couldn't have fallen unconscius from the bee stings, otherwise she would not have been able to run away from the beehive, and bees would have stung her all over.
So, that's at least one injury that was more severe than the bee stings, and that is using the laws of LBT, not laws of reality.