Custom Structure Permalinks not working

A little background first. I am working with 3 CPTs, which each have categories and subcategories. I have set up the Custom Structure Permalink as. %category% %postname%

For CPT A, I noticed that the permalink structure was as follows: http://www.xyz.com/CPTA/subcategory/postname

For CPT B, I noticed that the permalink structure was as follows: http://www.xyz.com/CPTB/category/postname

I thought it was very strange that for one CPT shows subcategories after the CPT and the other shows the category.

I was looking at this, because I would like the permalink to be as follows: domain/CPT/category/subcategory/postname. Not only for SEO, but also for retargeting.

Anyway, I removed the Custom Structure and then set it up again. But I have made the problem worse. Now the permalink structure is as follows: http://www.xyz.com/CPT/postname. Category or subcategory has disappeared.

I am sure I did something, but two questions:

1) How can I have categories again?
2) Is it possible to do the following: domain/CPT/category/subcategory/postname

Thanks in advance.