Was propably badly cut in the first place. It sounds as though the gutter was cut too short or not quite square where it rests in the joint. You will find that if there is movement ( which you have), it will be almost impossible to clean the joint and expect the silicone to hold it as you will only have a few mm overlap.
Idealy as guttering is so cheap it would be nice to replace the whole lot. But in the past when I have had this problem, if money has been an issue where a customer was involved, I have usualy solved it fairly simply and cheaply.
Clean up the joint area thouroughly as well as 75mm of the inside of the gutter on either side of the joint and re-assemble it in place with the clips in place.
Get a 2 mm drill bit and drill through the centre of the overlap. Fit a small stainless self tapper straight through the gutter from the inside pointing out. It may protrude a little but that will hold the joint together.
Now the important bit. Get some 150mm flashband and fit it inside the gutter overlaping the joint by 75mm on either side. It will stick like the preverbial to the clean surface, so dont get it wrong.
The clean dry surfaces are the key to success with this method.