Neural network outputs are not probabilities. I think that's the main lesson here.
The issue at hand is training them on overlapping classes :-)
I will shut up now, sorry for nitpicking.
But, I'm pretty sure the assumptions of logistic regression are even stronger than just that. The inputs are assumed to be independent given the output class, and the log odds of the output vary as a linear function of each input. The first one is essentially the naive Bayes assumption, and the second one is completely unreasonable for almost any problem ever (roughly equivalent to assuming every dataset has a multivariate normal distribution). If they are both correct, though, you get a perfectly good Bayesian posterior probability of each output class.
I think the lesson is that gradient descent will build a decent function approximation out of pretty much anything powerful enough, which is why neural networks still work even when probability theory has been thrown completely out the window.
A visual classifier that identify "4 moving things" might indicate some kind of land animal, or slow motion video of a Dragonfly in flight.
Sample/"evidence"-based reasoning will always have these kind of odd inconsistencies - I'm not sure if mapping such output to a logic model is an improvement. It might be - to take output from a classifier like this, and plug it into an expert system like a Prolog/datalog database or something. Or it might just end up being just as limited as those systems already are.
But when one says "tiger implies terrestrial mammal (or animal)", one is really talking about ontologies -- perhaps training the classifier to come up with things like "90% sure four legs, 60% sure fur" and plugging that into a logic based system would yield good hybrid systems?
I do think one would then loose the "magic" effectiveness of these pure(ish) learning systems though? Perhaps someone more familiar with the domains might shed some light?