i think i know what hte problem is and how to avoid, but not how to solve it
i ran into it today when modelling a house, basically, ur trying to split an object that has already been split so many times in different places. like with a cube, if you want to have 2 faces being made from one original face, then you would normally make one split right? but playing it safe you should split all the way around the cube in the same direction, that way u can avoid problems like this one where you've got unfinished splits as it were
thats my problem anyway
try not to split in unnessecary places, and when you do, makes sure its the split starts, goes all the way around and comes back to the starting point

that was very hard to explain :S