Problems during repotting. Help please!

[Zaskia]

Hello, I bought this Phalaenopsis orchid in January and it looked like it was doing great. There were lots of new roots growing, new leaves, a new flower spike and a new branch on one of the initial spikes.

I saw some white spots in the medium so decided to repot it. I now have 2 problems.

First, there was still a plug in the middle and the medium seemed quite broken down. It looks like quite a few roots are on their way to rotting? What should I do about them?

Second... it was my first time repotting and I injured the orchid's roots. There are a few that broke mid length but are still attached to the first part. Should I remove the part that is broken?

Thank you in advance!