EDIT: these areas did not have side face edges matching the top faces properly, so I had an idea.... replace those side faces with a single one that would not clash with the seams of all edges on the top (and bottom).

1- create new boundary patch/face that merges the side faces through the bad area:

2- replace the side faces with the single boundary patch/face:

3- add fillet again.... and this worked here for the bad area, see file attached:

Similar thread I found later that shows a similar approach:
https://forums.autodesk.com/t5/inventor-forum/help-identical-corner-won-t-fillet/td-p/6382845