Turn off "trim" when building the fillets and then hide the fillets and take a good close look at the COS's on the surfaces you want trimmed. You'll see gaps in the COS's or that they don't go all the way to the surface edges. This means there are gaps in the fillet surfaces (or they don't extend far enough at the ends) as they are created. To get it all fixed is a process with multiple solutions, BUT I would suggest starting by making sure all your original surfaces have tight positional and tangency accuracy to each other so you know that's not a problem going forward. Set all your modeling tolerances tight (you won't regret it). COS tolerance setting should be tight so that a fillet boundary edge creates an accurate and equivalent trim COS. THEN investigate the COS gaps and close the gaps or bridge them.
