One of the reasons this happens - as far as I can tell from my own writing - is too much focus on a character's primary trait. Real people tend to be living breathing bundles of contradiction. A kind person might well be cruel if stressed. A tolerant person may have a secret hatred for something. Human beings often think one thing and do another without even realising it. Cognitive dissonance is part of the human condition.
But if you make your characters too contradictory they'll be too confusing for the reader. Random personalities, like coincidence, are perceived as unrealistic in fiction even though both are common in reality. Characters, like dialogue, need to capture the essence of reality without the confusion of reality.
They also need to be likable without being perfect, or unlikable without be irredeemable - if a character isn't a mix of good and bad people will find them shallow.
All this can be bloody hard to balance.
The other reason it happens (again my opinion) is that I know my characters and their quirks, foibles and negative traits so well that I don't always notice when they're missing from what is written. It's just so obvious to me. Putting too much emphasis on certain behavorial traits like tongue tapping or a certain turn of phrase can also be an hindrance. They'll make a character recognisable - but that's not the same as deep.
So what to do?
One good piece of advice I've found in several places is 'inner conflict'. That is the character should want two mutually exclusive things. The things can be external - they can even be part of the external conflict, but they must have an internal effect. The internal conflict comes from the character's reaction to their dilemma.
Another good thing (also from multiple places) is to list the character's various traits - both good and bad - somewhere and what sort of situations are liable to trigger them. Then make sure that you write a scene for all of them at some point. In the end not all such things will be suitable for the plot, but if you've got them you can sort in the suitable ones and cut the rest. As long as you keep a balance.
- Writing Fictional Characters defines the above in terms of commonality, originality, dichotomy, desire, and peculiarity. This is a very good way to put it. Though I think the explanations could be a little more engaging.
- How to Create a Character is an interesting approach. It's not the one I use - but I do see where it can be useful and starting with what your character wants is certainly a good point.
- Building Fictional Characters. The chart and questions she's created are useful, and she has a load of helpful links.
- Character Development in Fiction is very detailed and goes beyond simply developing characters. It's interesting reading, and amusing for the author's comments on their first published novel and how bad it was.
Oh and if you're wondering I did manage to write a little over my 250 word target before bed last night.