Again - this is only in career mode.
Just so everyone understands what is happening, let's take Alex Hales for example.
In Munkeymomo's Notts team (the one being used in the above screenshot), he is the 9th player in the list for Notts.
In the on-disc Notts, the 9th player is 'P. Fitzpatrick' (Paul Franks in real life), and P. Fitzpatrick's skills classify him as a 2 helmet bowler. On the on-disc roster, the correct Alex Hales link is 12th. The disparity is caused by Munkeymomo uploading a more up to date roster than the on-disc roster.
The issue is, that Hales is effectively linked to P. Fitzpatrick in career mode, because they are both 9th on their respective teams. Hales becomes a bowler. He keeps the name, face, kit etc. But he picks up the attributes/skills of P. Fitzpatrick in career mode only.
I can't make it much simpler than that. That is what is happening, and that is what Big Ant are trying to fix. It is not being ignored.