> I did question it and was told that we don't want to completely remove the incentive for educated guessing.

So... you were told some unmotivated nonsense?

On an item with four answers, +1 for a correct answer and -0.25 for a wrong answer means that in expectation you will receive 0.0625 points for a completely uneducated guess. The only correct adjustment you can make is to dock 0.33(3...) for a wrong answer, in which case an uneducated guess is worth 0.0000 points and a minimally-educated guess, one in which you're capable of eliminating just one of the four answers, is worth... 0.0833(3...) points.

> I think the real reason is that our questions are usually N=4, negative marks of 0.25 allows for quick adding.

You think adding fourths is easy, but adding thirds is hard? If you really believe that, it'd be simple enough to add fifth choices to your questions.

Are you sure the real reason isn't just that nobody ever bothered to put any thought into what they were doing?