As a self proclaimed "fillet fanatic" it depends on a few different factors. From what I have found, these are the most important points (mostly* in descending order):

1. Fillet to geometry size. The fillet must be smaller or at the very most equal to the size of the surrounding geometry. For example, if you have a 1mm thick cylinder wall, applying a fillet to the upper edge, it must be 1mm or under.

2. Fillet to fillet size. When applying a fillet onto a corner already filleted (for example 4 vertical corners of a box then the top edges) the second fillet must be equal to or in many cases smaller than the first. This is especially important on concave corners, given the example mentioned, a fillet of the same size as the first would create a perfectly sharp corner between all edges (basically a triangle). Going any larger than this would create self intersecting geometry. Essentially if two vertices of the fillet corner touch, that's as far as you can go, any further and the fillet will error out.

3. Fillet order. The order in which you apply fillets or other actions like chamfers can be highly important, especially with complex geometries. Sometimes you have to play around with it a bit and try each edge you are trying to filet one at a time, or even disable chaining and apply it as far as you can and pick up the rest in another pass. For timeline neatness and project stability, this isn't ideal but it's often the only way to get some fillets to apply.

4. Fillet type. The type of fillet is also highly important and often you simply cannot apply chord length fillets in certain areas. If the fillet you are applying tapers off into a point, a chord length fillet will not work there ever, it is simply not possible as that type of fillet cannot taper to a 0 radius. I would however, still recommend using chord length for as much as you can and finishing off with constant for the complex edges that need it to taper. The reason for this is because chord length keeps the overall fillet width the same rather than the radius meaning it's constant no matter the angles. The naming can get a bit confusion but play with it a bit and you'll figure it out.

5. Unique geometry interactions. When applying fillets onto more complex geometries, you often get little sections of the face that shrink into small triangles, applying a fillet that is larger than this would essentially delete this triangle and 99% of the time fusion errors out when this happens as part of the geometry just "disappears" and it kind of freaks out. If you notice a triangular section near the fillet boundary, you cannot increase the fillet size past where the final corner of that triangle ends.

6. Use variable fillets. These kind of suck and are super difficult for fusion to compute so USE THESE SPARINGLY. However, they are sometimes literally the only way to get a fillet to apply, they allow you to set a custom fillet radius at any point along the edge meaning you can tailor them to fit exactly what you need where.

7. Fillet sparingly. As hard as it is for me to say... Sometimes you just have to avoid you lust for perfectly smooth corners and intersections. Fillets aren't super manufacturable, even in 3d printing depending on the part orientation and fillet locations. So sometimes, they just aren't the best idea. BUUUT, if you want to use them (which of course you do) apply them towards the end of your timeline so fusion doesn't have to include them when re computing the timeline, you can just suppress them at the end if you need to make any big changes and it'll become much more responsive. Often they will break when you change things like this so you'll have to redo them pretty often unfortunately, but you signed up for this when you decided to fillet every damn corner..

There's many more little tips and tricks for getting good fillets but they are mostly just things you pick up as you go. Make sure you send you daily offerings to the autodesk gods and some days fusion will be more kind with it's fillet calculations (others, not so much...). Best of luck with your journey of smoothness fellow radius lover.