Firstly, if you want a roughing pass and a finishing pass, you need two toolpaths. Usual approach is to have a small offset, pocket up to that for the first path, then do a Contour cut right to the final size.
Secondly, you are running into the ‘Pocketing Bug’. No ETA for a fix, only work around is too revert to an earlier version of CC.
https://community.carbide3d.com/t/bug-pocket-operations-cutting-as-slots/53457/15